1
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Lu P, Wu J, Zhang W. Identifying circRNA-disease association based on relational graph attention network and hypergraph attention network. Anal Biochem 2024; 694:115628. [PMID: 39069246 DOI: 10.1016/j.ab.2024.115628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/11/2024] [Accepted: 07/18/2024] [Indexed: 07/30/2024]
Abstract
In recent years, with the in-depth study of circRNA, scholars have begun to discover a synergistic relationship between circRNA and microorganisms. Traditional wet lab experiments in biology require expensive financial, material, and human resources to investigate the relationship between circRNA and diseases. Therefore, we propose a new predictive model for inferring the association between circRNA and diseases, called HAGACDA. Specifically, we first aggregate the unique features of circRNA and diseases themselves through singular value decomposition, Pearson similarity, and the biological information characteristics of circRNA and diseases. Utilizing the competitive relationships between miRNA and other microorganisms, we construct a circRNA-miRNA-disease multi-source heterogeneous network. Subsequently, we use a relational graph attention network to aggregate features based on the structural connections between different nodes. To address the inherent limitations in capturing high-order patterns in edge sets, we integrate a hypergraph attention network to extract features of circRNA and diseases. Finally, association prediction scores for node pairs are obtained through a multilayer perceptron. We conducted a comprehensive analysis of the model, including comparative experiments and case studies. Experimental results demonstrate that our model accurately predicts the association between circRNA and diseases.
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Affiliation(s)
- PengLi Lu
- School of Computer and Communication, Lanzhou University of Technology, Lanzhou, 730050, Gansu, PR China.
| | - Jinkai Wu
- School of Computer and Communication, Lanzhou University of Technology, Lanzhou, 730050, Gansu, PR China
| | - Wenqi Zhang
- School of Computer and Communication, Lanzhou University of Technology, Lanzhou, 730050, Gansu, PR China
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2
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Conn VM, Chinnaiyan AM, Conn SJ. Circular RNA in cancer. Nat Rev Cancer 2024; 24:597-613. [PMID: 39075222 DOI: 10.1038/s41568-024-00721-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/13/2024] [Indexed: 07/31/2024]
Abstract
Over the past decade, circular RNA (circRNA) research has evolved into a bona fide research field shedding light on the functional consequence of this unique family of RNA molecules in cancer. Although the method of formation and the abundance of circRNAs can differ from their cognate linear mRNA, the spectrum of interacting partners and their resultant cellular functions in oncogenesis are analogous. However, with 10 times more diversity in circRNA variants compared with linear RNA variants, combined with their hyperstability in the cell, circRNAs are equipped to influence every stage of oncogenesis. This is an opportune time to address the breadth of circRNA in cancer focused on their spatiotemporal expression, mutations in biogenesis factors and contemporary functions through each stage of cancer. In this Review, we highlight examples of functional circRNAs in specific cancers, which satisfy critical criteria, including their physical co-association with the target and circRNA abundance at stoichiometrically valid quantities. These considerations are essential to develop strategies for the therapeutic exploitation of circRNAs as biomarkers and targeted anticancer agents.
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Affiliation(s)
- Vanessa M Conn
- Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, South Australia, Australia
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Simon J Conn
- Flinders Health and Medical Research Institute, College of Medicine and Public Health, Flinders University, South Australia, Australia.
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3
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Wu J, Lu P, Zhang W. Predicting associations between CircRNA and diseases through structure-aware graph transformer and path-integral convolution. Anal Biochem 2024; 692:115554. [PMID: 38710353 DOI: 10.1016/j.ab.2024.115554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 04/27/2024] [Accepted: 04/30/2024] [Indexed: 05/08/2024]
Abstract
A series of biological experiments has demonstrated that circular RNAs play a crucial regulatory role in cellular processes and may be potentially associated with diseases. Uncovering these connections helps in understanding potential disease mechanisms and advancing the development of treatment strategies. However, in biology, traditional experiments face limitations in terms of efficiency and cost, especially when enumerating possible associations. To address these limitations, several computational methods have been proposed, but existing methods only measure from a nodal perspective and cannot capture structural similarities between edges. In this study, we introduce an advanced computational method called SATPIC2CD for analyzing potential associations between circular RNAs and diseases. Specifically, we first employ an Structure-Aware Graph Transformer (SAT), which extracts five predefined metapath representations before calculating attention. This adaptive network integrates structural information into the original self-attention by aggregating information within and between paths. Subsequently, we use Path Integral Convolutional Networks (PACN) to integrate feature information for all path weights between two nodes. Afterward, we complement the network node features with feature loss and feature smoothing using Gated Recurrent Units (GRU) and node centrality. Finally, a Multi-Layer Perceptron (MLP) is employed to obtain the ultimate prediction scores for each circular RNA-disease pair. SATPIC2CD performs remarkably well, with an accuracy of up to 0.9715 measured by the Area Under the Curve (AUC) in a 5-fold cross-validation, surpassing other comparative models. Case studies further emphasize the high precision of our method in identifying circular RNA-disease associations, laying a solid foundation for guiding future biological research efforts.
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Affiliation(s)
- Jinkai Wu
- School of Computer and Communication, Lanzhou University of Technology, Lanzhou, 730050, Gansu, PR China
| | - PengLi Lu
- School of Computer and Communication, Lanzhou University of Technology, Lanzhou, 730050, Gansu, PR China.
| | - Wenqi Zhang
- School of Computer and Communication, Lanzhou University of Technology, Lanzhou, 730050, Gansu, PR China
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4
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Zhao J, Ma Y, Zheng X, Sun Z, Lin H, Du C, Cao J. Bladder cancer: non-coding RNAs and exosomal non-coding RNAs. Funct Integr Genomics 2024; 24:147. [PMID: 39217254 DOI: 10.1007/s10142-024-01433-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Revised: 08/15/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024]
Abstract
Bladder cancer (BCa) is a highly prevalent type of cancer worldwide, and it is responsible for numerous deaths and cases of disease. Due to the diverse nature of this disease, it is necessary to conduct significant research that delves deeper into the molecular aspects, to potentially discover novel diagnostic and therapeutic approaches. Lately, there has been a significant increase in the focus on non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), due to their growing recognition for their involvement in the progression and manifestation of BCa. The interest in exosomes has greatly grown due to their potential for transporting a diverse array of active substances, including proteins, nucleic acids, carbohydrates, and lipids. The combination of these components differs based on the specific cell and its condition. Research indicates that using exosomes could have considerable advantages in identifying and forecasting BCa, offering a less invasive alternative. The distinctive arrangement of the lipid bilayer membrane found in exosomes is what makes them particularly effective for administering treatments aimed at managing cancer. In this review, we have tried to summarize different ncRNAs that are involved in BCa pathogenesis. Moreover, we highlighted the role of exosomal ncRNAs in BCa.
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Affiliation(s)
- Jingang Zhao
- Department of Urology, Hangzhou Mingzhou Hospital, Hangzhou, 311215, Zhe'jiang, China
| | - Yangyang Ma
- Department of Urology, Hangzhou Mingzhou Hospital, Hangzhou, 311215, Zhe'jiang, China
| | - Xiaodong Zheng
- Department of the First Surgery, Zhejiang Provincial Corps Hospital of Chinese People's Armed Police Force, Hangzhou, 310051, Zhe'jiang, China
| | - Zhen Sun
- Department of the First Surgery, Zhejiang Provincial Corps Hospital of Chinese People's Armed Police Force, Hangzhou, 310051, Zhe'jiang, China
| | - Hongxiang Lin
- Department of Urology, Ganzhou Donghe Hospital, Ganzhou, 341000, Jiang'xi, China
| | - Chuanjun Du
- Department of Urology, Second Affiliated Hospital of Zhejiang University College of Medicine, Hangzhou, 310009, Zhe'jiang, China
| | - Jing Cao
- Department of Urology, Hangzhou Mingzhou Hospital, Hangzhou, 311215, Zhe'jiang, China.
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5
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He S, Bing J, Zhong Y, Zheng X, Zhou Z, Wang Y, Hu J, Sun X. PlantCircRNA: a comprehensive database for plant circular RNAs. Nucleic Acids Res 2024:gkae709. [PMID: 39189447 DOI: 10.1093/nar/gkae709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/11/2024] [Accepted: 08/02/2024] [Indexed: 08/28/2024] Open
Abstract
Circular RNAs (circRNAs) represent recently discovered novel regulatory non-coding RNAs. While they are present in many eukaryotes, there has been limited research on plant circRNAs. We developed PlantCircRNA (https://plant.deepbiology.cn/PlantCircRNA/) to fill this gap. The two most important features of PlantCircRNA are (i) it incorporates circRNAs from 94 plant species based on 39 245 RNA-sequencing samples and (ii) it imports the original AtCircDB and CropCircDB databases. We manually curated all circRNAs from published articles, and imported them into the database. Furthermore, we added detailed information of tissue as well as abiotic stresses to the database. To help users understand these circRNAs, the database includes a detection score to measure their consistency and a naming system following the guidelines recently proposed for eukaryotes. Finally, we developed a comprehensive platform for users to visualize, analyze, and download data regarding specific circRNAs. This resource will serve as a home for plant circRNAs and provide the community with unprecedented insights into these mysterious molecule.
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Affiliation(s)
- Shutian He
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Jianhao Bing
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Yang Zhong
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Xiaoyang Zheng
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Ziyu Zhou
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Yifei Wang
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Jiming Hu
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Xiaoyong Sun
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
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Peng D, Wei C, Jing B, Yu R, Zhang Z, Han L. A novel protein encoded by circCOPA inhibits the malignant phenotype of glioblastoma cells and increases their sensitivity to temozolomide by disrupting the NONO-SFPQ complex. Cell Death Dis 2024; 15:616. [PMID: 39183343 PMCID: PMC11345445 DOI: 10.1038/s41419-024-07010-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 08/10/2024] [Accepted: 08/16/2024] [Indexed: 08/27/2024]
Abstract
Glioblastoma (GBM) represents a primary malignant brain tumor. Temozolomide resistance is a major hurdle in GBM treatment. Proteins encoded by circular RNAs (circRNAs) can modulate the sensitivity of multiple tumor chemotherapies. However, the impact of circRNA-encoded proteins on GBM sensitivity to temozolomide remains unknown. Herein, we discover a circRNA (circCOPA) through the circRNA microarray profile in GBM samples, which can encode a novel 99 amino acid protein (COPA-99aa) through its internal ribosome entry site. Functionally, circCOPA overexpression in GBM cells inhibits cell proliferation, migration, and invasion in vitro and growth in vivo. Rather than itself, circCOPA mainly functions as a suppressive effector by encoding COPA-99aa. Moreover, we reveal that circCOPA is downregulated in GBM tissues and high expression of circCOPA is related to a better prognosis in GBM patients. Mechanistically, a heteromer of SFPQ and NONO is required for double-strand DNA break repair. COPA-99aa disrupts the dimerization of NONO and SFPQ by separately binding with the NONO and SFPQ proteins, thus resulting in the inhibition of proliferation or invasion and the increase of temozolomide-induced DNA damage in GBM cells. Collectively, our data suggest that circCOPA mainly contributes to inhibiting the GBM malignant phenotype through its encoded COPA-99aa and that COPA-99aa increases temozolomide-induced DNA damage by interfering with the dimerization of NONO and SFPQ. Restoring circCOPA or COPA-99aa may increase the sensitivity of patients to temozolomide.
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Affiliation(s)
- Dazhao Peng
- Tianjin Neurological Institute, Key Laboratory of Post-Neuro injury, Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China
| | - Cheng Wei
- Tianjin Neurological Institute, Key Laboratory of Post-Neuro injury, Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China
| | - Boyuan Jing
- Tianjin Neurological Institute, Key Laboratory of Post-Neuro injury, Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China
| | - Runze Yu
- Tianjin Neurological Institute, Key Laboratory of Post-Neuro injury, Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China
| | - Zhenyu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| | - Lei Han
- Tianjin Neurological Institute, Key Laboratory of Post-Neuro injury, Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin, China.
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7
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Zuo Y, Liu W, Jin Y, Pan Y, Fan T, Fu X, Guo J, Tan S, He J, Yang Y, Li Z, Yang C, Peng Y. C2CDB: an advanced platform integrating comprehensive information and analysis tools of cancer-related circRNAs. BIOINFORMATICS ADVANCES 2024; 4:vbae112. [PMID: 39246384 PMCID: PMC11379471 DOI: 10.1093/bioadv/vbae112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/04/2024] [Accepted: 08/14/2024] [Indexed: 09/10/2024]
Abstract
Motivation Circular RNAs (circRNAs) play important roles in gene expression and their involvement in tumorigenesis is emerging. circRNA-related database is a powerful tool for researchers to investigate circRNAs. However, existing databases lack advanced platform integrating comprehensive information and analysis tools of cancer-related circRNAs. Results We developed a comprehensive platform called CircRNA to Cancer Database (C2CDB), encompassing 318 158 cancer-related circRNAs expressed in tumors and adjacent tissues across 30 types of cancers. C2CDB provides basic details such as sequence and expression levels of circRNAs, as well as crucial insights into biological mechanisms, including miRNA binding, RNA-binding protein interaction, coding potential, base modification, mutation, and secondary structure. Moreover, C2CDB collects an extensive compilation of published literature on cancer circRNAs, extracting and presenting pivotal content encompassing biological functions, underlying mechanisms, and molecular tools in these studies. Additionally, C2CDB offers integrated tools to analyse three potential mechanisms: circRNA-miRNA ceRNA interaction, circRNA encoding, and circRNA biogenesis, facilitating investigators with convenient access to highly reliable information. To enhance clarity and organization, C2CDB has meticulously curated and integrated the previously chaotic nomenclature of circRNAs, addressing the prevailing confusion and ambiguity surrounding their designations. Availability and implementation C2CDB is freely available at http://pengyonglab.com/c2cdb.
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Affiliation(s)
- Yuanli Zuo
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Wenrong Liu
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Yang Jin
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Yitong Pan
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Ting Fan
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Xin Fu
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Jiawei Guo
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Shuangyan Tan
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Juan He
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Yang Yang
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Zhang Li
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Chenyu Yang
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Yong Peng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
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8
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Wang XF, Yu CQ, You ZH, Wang Y, Huang L, Qiao Y, Wang L, Li ZW. BEROLECMI: a novel prediction method to infer circRNA-miRNA interaction from the role definition of molecular attributes and biological networks. BMC Bioinformatics 2024; 25:264. [PMID: 39127625 DOI: 10.1186/s12859-024-05891-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
Circular RNA (CircRNA)-microRNA (miRNA) interaction (CMI) is an important model for the regulation of biological processes by non-coding RNA (ncRNA), which provides a new perspective for the study of human complex diseases. However, the existing CMI prediction models mainly rely on the nearest neighbor structure in the biological network, ignoring the molecular network topology, so it is difficult to improve the prediction performance. In this paper, we proposed a new CMI prediction method, BEROLECMI, which uses molecular sequence attributes, molecular self-similarity, and biological network topology to define the specific role feature representation for molecules to infer the new CMI. BEROLECMI effectively makes up for the lack of network topology in the CMI prediction model and achieves the highest prediction performance in three commonly used data sets. In the case study, 14 of the 15 pairs of unknown CMIs were correctly predicted.
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Affiliation(s)
- Xin-Fei Wang
- School of Information Engineering, Xijing University, Xi'an, China
| | - Chang-Qing Yu
- School of Information Engineering, Xijing University, Xi'an, China.
| | - Zhu-Hong You
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China.
| | - Yan Wang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China.
- School of Artificial Intelligence, Jilin University, Changchun, China.
| | - Lan Huang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Yan Qiao
- College of Agriculture and Forestry, Longdong University, Qingyang, China
| | - Lei Wang
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, China
- Guangxi Academy of Sciences, Nanning, China
| | - Zheng-Wei Li
- School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, China
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9
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Mei S, Ma X, Zhou L, Wuyun Q, Cai Z, Yan J, Ding H. Circular RNA in Cardiovascular Diseases: Biogenesis, Function and Application. Biomolecules 2024; 14:952. [PMID: 39199340 PMCID: PMC11352787 DOI: 10.3390/biom14080952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 07/31/2024] [Accepted: 08/05/2024] [Indexed: 09/01/2024] Open
Abstract
Cardiovascular diseases pose a significant public health challenge globally, necessitating the development of effective treatments to mitigate the risk of cardiovascular diseases. Recently, circular RNAs (circRNAs), a novel class of non-coding RNAs, have been recognized for their role in cardiovascular disease. Aberrant expression of circRNAs is closely linked with changes in various cellular and pathophysiological processes within the cardiovascular system, including metabolism, proliferation, stress response, and cell death. Functionally, circRNAs serve multiple roles, such as acting as a microRNA sponge, providing scaffolds for proteins, and participating in protein translation. Owing to their unique properties, circRNAs may represent a promising biomarker for predicting disease progression and a potential target for cardiovascular drug development. This review comprehensively examines the properties, biogenesis, and potential mechanisms of circRNAs, enhancing understanding of their role in the pathophysiological processes impacting cardiovascular disease. Furthermore, the prospective clinical applications of circRNAs in the diagnosis, prognosis, and treatment of cardiovascular disease are addressed.
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Affiliation(s)
- Shuai Mei
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jiefang Ave., Wuhan 430030, China; (S.M.); (X.M.); (L.Z.); (Q.W.); (Z.C.)
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Xiaozhu Ma
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jiefang Ave., Wuhan 430030, China; (S.M.); (X.M.); (L.Z.); (Q.W.); (Z.C.)
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Li Zhou
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jiefang Ave., Wuhan 430030, China; (S.M.); (X.M.); (L.Z.); (Q.W.); (Z.C.)
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Qidamugai Wuyun
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jiefang Ave., Wuhan 430030, China; (S.M.); (X.M.); (L.Z.); (Q.W.); (Z.C.)
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Ziyang Cai
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jiefang Ave., Wuhan 430030, China; (S.M.); (X.M.); (L.Z.); (Q.W.); (Z.C.)
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Jiangtao Yan
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jiefang Ave., Wuhan 430030, China; (S.M.); (X.M.); (L.Z.); (Q.W.); (Z.C.)
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Hu Ding
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jiefang Ave., Wuhan 430030, China; (S.M.); (X.M.); (L.Z.); (Q.W.); (Z.C.)
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
- Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095# Jiefang Ave., Wuhan 430030, China
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10
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Li D, Min Z, Guo J, Chen Y, Zhang W. ExpOmics: a comprehensive web platform empowering biologists with robust multi-omics data analysis capabilities. Bioinformatics 2024; 40:btae507. [PMID: 39128019 PMCID: PMC11343375 DOI: 10.1093/bioinformatics/btae507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 07/18/2024] [Accepted: 08/09/2024] [Indexed: 08/13/2024] Open
Abstract
MOTIVATION High-throughput technologies yield a broad spectrum of multi-omics datasets, which offer unparalleled insights into complex biological systems. However, effectively analyzing this diverse array of data presents challenges, considering factors such as species diversity, data types, costs, and limitations of the available tools. RESULTS Herein, we present ExpOmics, a comprehensive web platform featuring 7 applications and 4 toolkits, with 28 customizable analysis functions spanning various analyses of differential expression, co-expression, Weighted Gene Co-expression Network Analysis (WGCNA), feature selection, and functional enrichment. ExpOmics allows users to upload and explore multi-omics data without organism restrictions, supporting various expression data, including genes, mRNAs, lncRNAs, miRNAs, circRNAs, piRNAs, and proteins and is compatible with diverse gene nomenclatures and expression values. Moreover, ExpOmics enables users to analyze 22 427 transcriptomic datasets of 196 cancer subtypes sourced from 63 projects of The Cancer Genome Atlas Program (TCGA) to identify cancer biomarkers. The analysis results from ExpOmics are presented in high-quality graphical formats suitable for publication and are available for free download. A case study using ExpOmics identified two potential oncogenes, SERPINE1 and SLC43A1, that may regulate colorectal cancer through distinct biological processes. In summary, ExpOmics can serves as a robust platform for global researchers to explore multi-omics data, gain biological insights, and formulate testable hypotheses. AVAILABILITY AND IMPLEMENTATION ExpOmics is available at http://www.biomedical-web.com/expomics.
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Affiliation(s)
- Douyue Li
- The Key Laboratory of Advanced Interdisciplinary Studies, The First Affiliated Hospital of Guangzhou Medical University, GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou 510182, People’s Republic of China
| | - Zhuochao Min
- School of Zoology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Jia Guo
- The Key Laboratory of Advanced Interdisciplinary Studies, The First Affiliated Hospital of Guangzhou Medical University, GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou 510182, People’s Republic of China
| | - Yubin Chen
- The Key Laboratory of Advanced Interdisciplinary Studies, The First Affiliated Hospital of Guangzhou Medical University, GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou 510182, People’s Republic of China
| | - Wenliang Zhang
- The Key Laboratory of Advanced Interdisciplinary Studies, The First Affiliated Hospital of Guangzhou Medical University, GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macao Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou 510182, People’s Republic of China
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, People’s Republic of China
- Department of Bioinformatics, Outstanding Biotechnology Co., Ltd-Shenzhen, Shenzhen 518026, People’s Republic of China
- Department of Pediatrics, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518053, People’s Republic of China
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11
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Lin H, Cui Z, E T, Xu H, Wang D, Wang P, Ruan X, Liu L, Xue Y. M6A-methylated circPOLR2B forms an R-loop and regulates the biological behavior of glioma stem cells through positive feedback loops. Cell Death Dis 2024; 15:554. [PMID: 39090090 PMCID: PMC11294345 DOI: 10.1038/s41419-024-06946-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 07/18/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024]
Abstract
Glioma is the most common primary brain tumor, and targeting glioma stem cells (GSCs) has become a key aspect of glioma treatment. In this study, we discovered a molecular network in which circRNA forms an R-loop structure with its parental gene to regulate the biological behavior of GSCs. Genes with abnormal expression in GSCs were screened using RNA-seq and circRNA microarray analyses. The study results showed that high expression of YTHDC1 in GSCs promoted the transportation of N6-methyladenosine (m6A)-modified circPOLR2B from the nucleus to the cytoplasm. Decreased circPOLR2B levels in the nucleus resulted in fewer R-loop structures formed with its parental gene POLR2B. This reduction in R-loop structures relieved the inhibitory effect on POLR2B transcription and upregulated PBX1 expression through alternative polyadenylation (APA) action, thereby promoting the malignant biological behavior of GSCs. Knockdown of YTHDC1, POLR2B, and PBX1 reduced xenograft tumor volume and prolonged the survival of nude mice. The YTHDC1/circPOLR2B/POLR2B/PBX1 axis plays a regulatory role in the biological behavior of GSCs, offering potential targets and novel strategies for the treatment of glioma.
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Affiliation(s)
- Hongda Lin
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, China
| | - Zheng Cui
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, China
| | - Tiange E
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, China
| | - Hailing Xu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, China
| | - Di Wang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Liaoning Medical Surgery and Rehabilitation Robot Technology Engineering Research Center, Shenyang, China
| | - Ping Wang
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
| | - Xuelei Ruan
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
| | - Libo Liu
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
| | - Yixue Xue
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China.
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China.
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12
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Youness RA, Hassan HA, Abaza T, Hady AA, El Magdoub HM, Ali M, Vogel J, Thiersch M, Gassmann M, Hamdy NM, Aboouf MA. A Comprehensive Insight and In Silico Analysis of CircRNAs in Hepatocellular Carcinoma: A Step toward ncRNA-Based Precision Medicine. Cells 2024; 13:1245. [PMID: 39120276 PMCID: PMC11312109 DOI: 10.3390/cells13151245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/11/2024] [Accepted: 07/22/2024] [Indexed: 08/10/2024] Open
Abstract
Circular RNAs (circRNAs) are cardinal players in numerous physiological and pathological processes. CircRNAs play dual roles as tumor suppressors and oncogenes in different oncological contexts, including hepatocellular carcinoma (HCC). Their roles significantly impact the disease at all stages, including initiation, development, progression, invasion, and metastasis, in addition to the response to treatment. In this review, we discuss the biogenesis and regulatory functional roles of circRNAs, as well as circRNA-protein-mRNA ternary complex formation, elucidating the intricate pathways tuned by circRNAs to modulate gene expression and cellular processes through a comprehensive literature search, in silico search, and bioinformatics analysis. With a particular focus on the interplay between circRNAs, epigenetics, and HCC pathology, the article sets the stage for further exploration of circRNAs as novel investigational theranostic agents in the dynamic realm of HCC.
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Affiliation(s)
- Rana A. Youness
- Molecular Genetics Research Team (MGRT), Molecular Biology and Biochemistry Department, Faculty of Biotechnology, German International University (GIU), Cairo 11835, Egypt; (R.A.Y.); (H.A.H.); (T.A.)
| | - Hossam A. Hassan
- Molecular Genetics Research Team (MGRT), Molecular Biology and Biochemistry Department, Faculty of Biotechnology, German International University (GIU), Cairo 11835, Egypt; (R.A.Y.); (H.A.H.); (T.A.)
| | - Tasneem Abaza
- Molecular Genetics Research Team (MGRT), Molecular Biology and Biochemistry Department, Faculty of Biotechnology, German International University (GIU), Cairo 11835, Egypt; (R.A.Y.); (H.A.H.); (T.A.)
- Biotechnology Program, Institute of Basic and Applied Sciences (BAS), Egypt-Japan University of Science and Technology (E-JUST), New Borg El-Arab City 21934, Egypt
| | - Ahmed A. Hady
- Clinical Oncology Department, Faculty of Medicine, Mansoura University, Mansoura 35511, Egypt;
| | - Hekmat M. El Magdoub
- Biochemistry Department, Faculty of Pharmacy, Misr International University, Cairo 19648, Egypt;
| | - Mohamed Ali
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL 60637, USA;
- Clinical Pharmacy Department, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Johannes Vogel
- Zurich Center for Integrative Human Physiology and Institute of V. Physiology, University of Zurich, 8057 Zurich, Switzerland; (J.V.); (M.T.); (M.G.)
| | - Markus Thiersch
- Zurich Center for Integrative Human Physiology and Institute of V. Physiology, University of Zurich, 8057 Zurich, Switzerland; (J.V.); (M.T.); (M.G.)
| | - Max Gassmann
- Zurich Center for Integrative Human Physiology and Institute of V. Physiology, University of Zurich, 8057 Zurich, Switzerland; (J.V.); (M.T.); (M.G.)
| | - Nadia M. Hamdy
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abassia, Cairo 11566, Egypt
| | - Mostafa A. Aboouf
- Zurich Center for Integrative Human Physiology and Institute of V. Physiology, University of Zurich, 8057 Zurich, Switzerland; (J.V.); (M.T.); (M.G.)
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abassia, Cairo 11566, Egypt
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13
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Guo Y, Yi M. THGNCDA: circRNA-disease association prediction based on triple heterogeneous graph network. Brief Funct Genomics 2024; 23:384-394. [PMID: 37738503 DOI: 10.1093/bfgp/elad042] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/21/2023] [Accepted: 09/04/2023] [Indexed: 09/24/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of noncoding RNA molecules featuring a closed circular structure. They have been proved to play a significant role in the reduction of many diseases. Besides, many researches in clinical diagnosis and treatment of disease have revealed that circRNA can be considered as a potential biomarker. Therefore, understanding the association of circRNA and diseases can help to forecast some disorders of life activities. However, traditional biological experimental methods are time-consuming. The most common method for circRNA-disease association prediction on the basis of machine learning can avoid this, which relies on diverse data. Nevertheless, topological information of circRNA and disease usually is not involved in these methods. Moreover, circRNAs can be associated with diseases through miRNAs. With these considerations, we proposed a novel method, named THGNCDA, to predict the association between circRNAs and diseases. Specifically, for a certain pair of circRNA and disease, we employ a graph neural network with attention to learn the importance of its each neighbor. In addition, we use a multilayer convolutional neural network to explore the relationship of a circRNA-disease pair based on their attributes. When calculating embeddings, we introduce the information of miRNAs. The results of experiments show that THGNCDA outperformed the SOTA methods. In addition, it can be observed that our method gives a better recall rate. To confirm the significance of attention, we conducted extensive ablation studies. Case studies on Urinary Bladder and Prostatic Neoplasms further show THGNCDA's ability in discovering known relationships between circRNA candidates and diseases.
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Affiliation(s)
- Yuwei Guo
- School of Mathematics and Physics, China University of Geosciences, 388 Lumo Road, Hongshan District, 430074, Wuhan, Hubei, China
| | - Ming Yi
- School of Mathematics and Physics, China University of Geosciences, 388 Lumo Road, Hongshan District, 430074, Wuhan, Hubei, China
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14
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Li S, Zhang Y, Liu G, Song N, Ruan Z, Guo R, Tang Y, Cao X, Huang X, Gao T, Hao S, Wang Q, Chang T. Exploring the Roles of m6A-Modified circRNAs in Myasthenia Gravis Based on Multi-Omics Analysis. Mol Neurobiol 2024:10.1007/s12035-024-04352-9. [PMID: 39017976 DOI: 10.1007/s12035-024-04352-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024]
Abstract
Myasthenia gravis (MG) is an autoimmune disease mediated by autoantibodies. The important roles of circRNAs modified by m6A methylation have been reported in the pathogenesis of other autoimmune diseases, but remain unclear in MG. To address this point, we collected peripheral blood mononuclear cells from six MG patients and six healthy controls and performed m6A‑circRNA epitranscriptomic microarray and RNA sequencing. Differentially m6A-modified circRNAs and differentially expressed genes (DEGs) were analyzed. A network was constructed containing 17 circRNAs, 30 miRNAs, and 34 DEGs. The GSE85452 dataset was downloaded. DEGs that were differentially expressed in the GSE85452 dataset were selected as seed genes. Finally, four candidate m6A-modified circRNAs (hsa_circ_0084735, hsa_circ_0018652, hsa_circ_0025731, and hsa_circ_0030997) were identified through a random walk with restart. We found that they had different degree correlations with different immune cells. The results of MeRIP-qPCR showed that the m6A methylated levels of hsa_circ_0084735 and hsa_circ_0025731 were downregulated in MG patients, while the other two circRNAs were not significantly different between MG and control group. For the first time, we explored the pathogenesis of MG at the epigenetic transcriptome level. Our results will open new perspectives for MG research and identify potential biomarkers and therapeutic targets for MG.
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Affiliation(s)
- Shuang Li
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Yu Zhang
- Department of Neurosurgery, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Geyu Liu
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
- The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Na Song
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Zhe Ruan
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Rongjing Guo
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Yonglan Tang
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Xiangqi Cao
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Xiaoxi Huang
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Ting Gao
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Sijia Hao
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Qingqing Wang
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Ting Chang
- Department of Neurology, Tangdu Hospital, the Fourth Military Medical University, Xi'an, 710038, Shaanxi, China.
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15
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Lan S, Zhong G. Identification of a novel survival and immune microenvironment related ceRNA regulatory network for hepatocellular carcinoma based on circHECTD1. Heliyon 2024; 10:e33763. [PMID: 39040406 PMCID: PMC11261882 DOI: 10.1016/j.heliyon.2024.e33763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/24/2024] [Accepted: 06/26/2024] [Indexed: 07/24/2024] Open
Abstract
Background CircHECTD1 (circ_0031450) is highly expressed in hepatocellular carcinoma (HCC) tissues and may act as an oncogene. Its specific competitive endogenous RNA (ceRNA) mechanism remains to be further elucidated. Methods Several databases and online platforms, including pathway activity, immune checkpoint, and overall survival analyses, were used to predict targets, download datasets, and perform online analyses. The R software was used for differential gene expression analysis, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), clinical relevance, receiver operator characteristic curve, and single-cell analysis. Cytoscape software was used to construct ceRNAs, protein-protein interactions (PPI), and pivotal networks. Results The ceRNA, PPI, and pivotal networks were successfully constructed. Pathway enrichment analysis was mainly related to apoptosis, cell cycle, and epithelial-mesenchymal transition (EMT) pathways. Six pivotal targets related to survival, immune infiltration, immune checkpoints, clinical stage, and diagnosis of patients with HCC were identified. The recovery function and pathway enrichment results were consistent with previous results. Single-cell analysis suggested that the pivotal targets were highly expressed in T cells. Conclusion We successfully constructed a prognosis and immune microenvironment-related ceRNA network based on circHECTD1, providing new insights for diagnosing and treating HCC.
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Affiliation(s)
- Shuiqing Lan
- Department of Pain Management, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, 533000, China
| | - Guoqiang Zhong
- The Graduate School, Youjiang Medical University for Nationalities, Baise, Guangxi, 533000, China
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16
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Chaudhary U, Banerjee S. Decoding the Non-coding: Tools and Databases Unveiling the Hidden World of "Junk" RNAs for Innovative Therapeutic Exploration. ACS Pharmacol Transl Sci 2024; 7:1901-1915. [PMID: 39022352 PMCID: PMC11249652 DOI: 10.1021/acsptsci.3c00388] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 05/15/2024] [Accepted: 05/27/2024] [Indexed: 07/20/2024]
Abstract
Non-coding RNAs are pivotal regulators of gene and protein expression, exerting crucial influences on diverse biological processes. Their dysregulation is frequently implicated in the onset and progression of diseases, notably cancer. A profound comprehension of the intricate mechanisms governing ncRNAs is imperative for devising innovative therapeutic interventions against these debilitating conditions. Significantly, nearly 80% of our genome comprises ncRNAs, underscoring their centrality in cellular processes. The elucidation of ncRNA functions is pivotal for grasping the complexities of gene regulation and its implications for human health. Modern genome sequencing techniques yield vast datasets, stored in specialized databases. To harness this wealth of information and to understand the crosstalk of non-coding RNAs, knowledge of available databases is required, and many new sophisticated computational tools have emerged. These tools play a pivotal role in the identification, prediction, and annotation of ncRNAs, thereby facilitating their experimental validation. This Review succinctly outlines the current understanding of ncRNAs, emphasizing their involvement in disease development. It also highlights the databases and tools instrumental in classifying, annotating, and evaluating ncRNAs. By extracting meaningful biological insights from seemingly "junk" data, these tools empower scientists to unravel the intricate roles of ncRNAs in shaping human health.
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Affiliation(s)
- Uma Chaudhary
- Department of Biotechnology,
School of Biosciences and Technology, Vellore
Institute of Technology (VIT), Vellore, Tamil Nadu 632014, India
| | - Satarupa Banerjee
- Department of Biotechnology,
School of Biosciences and Technology, Vellore
Institute of Technology (VIT), Vellore, Tamil Nadu 632014, India
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17
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Zhao H, Xiong Y, Zhou Z, Xu Q, Zi Y, Zheng X, Chen S, Xiao X, Gong L, Xu H, Liu L, Lu H, Cui Y, Shao S, Zhang J, Ma J, Zhou Q, Ma D, Li X. A hidden proteome encoded by circRNAs in human placentas: Implications for uncovering preeclampsia pathogenesis. Clin Transl Med 2024; 14:e1759. [PMID: 38997803 PMCID: PMC11245404 DOI: 10.1002/ctm2.1759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 06/21/2024] [Accepted: 06/25/2024] [Indexed: 07/14/2024] Open
Abstract
BACKGROUND CircRNA-encoded proteins (CEPs) are emerging as new players in health and disease, and function as baits for the common partners of their cognate linear-spliced RNA encoded proteins (LEPs). However, their prevalence across human tissues and biological roles remain largely unexplored. The placenta is an ideal model for identifying CEPs due to its considerable protein diversity that is required to sustain fetal development during pregnancy. The aim of this study was to evaluate circRNA translation in the human placenta, and the potential roles of the CEPs in placental development and dysfunction. METHODS Multiomics approaches, including RNA sequencing, ribosome profiling, and LC-MS/MS analysis, were utilised to identify novel translational events of circRNAs in human placentas. Bioinformatics methods and the protein bait hypothesis were employed to evaluate the roles of these newly discovered CEPs in placentation and associated disorders. The pathogenic role of a recently identified CEP circPRKCB119aa in preeclampsia was investigated through qRT-PCR, Western blotting, immunofluorescence imaging and phenotypic analyses. RESULTS We found that 528 placental circRNAs bound to ribosomes with active translational elongation, and 139 were translated to proteins. The CEPs showed considerable structural homology with their cognate LEPs, but are more stable, hydrophobic and have a lower molecular-weight than the latter, all of which are conducive to their function as baits. On this basis, CEPs are deduced to be closely involved in placental function. Furthermore, we focused on a novel CEP circPRKCB119aa, and illuminated its pathogenic role in preeclampsia; it enhanced trophoblast autophagy by acting as a bait to inhibit phosphorylation of the cognate linear isoform PKCβ. CONCLUSIONS We discovered a hidden circRNA-encoded proteome in the human placenta, which offers new insights into the mechanisms underlying placental development, as well as placental disorders such as preeclampsia. Key points A hidden circRNA-encoded proteome in the human placenta was extensively identified and systematically characterised. The circRNA-encoded proteins (CEPs) are potentially related to placental development and associated disorders. A novel conserved CEP circPRKCB119aa enhanced trophoblast autophagy by inhibiting phosphorylation of its cognate linear-spliced isoform protein kinase C (PKC) β in preeclampsia.
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Affiliation(s)
- Huanqiang Zhao
- The Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Institute of Maternal and Child Medicine, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| | - Yu Xiong
- The Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Zixiang Zhou
- The Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Qixin Xu
- Institute of Maternal and Child Medicine, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| | - Yang Zi
- Institute of Maternal and Child Medicine, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| | - Xiujie Zheng
- Institute of Maternal and Child Medicine, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| | - Shiguo Chen
- Institute of Maternal and Child Medicine, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
| | - Xirong Xiao
- The Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Lili Gong
- The Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Huangfang Xu
- The Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Lidong Liu
- The Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Huiqing Lu
- The Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Yutong Cui
- The Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Shuyi Shao
- The Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Jin Zhang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jing Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Qiongjie Zhou
- The Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Duan Ma
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xiaotian Li
- The Shanghai Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Institute of Maternal and Child Medicine, Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong Province, China
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18
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Zhong Q, Jin S, Zhang Z, Qian H, Xie Y, Yan P, He W, Zhang L. Identification and verification of circRNA biomarkers for coronary artery disease based on WGCNA and the LASSO algorithm. BMC Cardiovasc Disord 2024; 24:305. [PMID: 38880872 PMCID: PMC11181640 DOI: 10.1186/s12872-024-03972-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 06/10/2024] [Indexed: 06/18/2024] Open
Abstract
BACKGROUND The role of circular RNAs (circRNAs) as biomarkers of coronary artery disease (CAD) remains poorly explored. This study aimed to identify and validate potential circulating circRNAs as biomarkers for the diagnosis of CAD. METHODS The expression profile of circRNAs associated with CAD was obtained from Gene Expression Omnibus (GEO) database. Differential expression analysis, weighted gene co-expression network analysis (WGCNA) and least absolute shrinkage and selection operation (LASSO) were employed to identify CAD-related hub circRNAs. The expression levels of these hub circRNAs were validated using qRT-PCR in blood samples from 100 CAD patients and 100 controls. The diagnostic performance of these circRNAs was evaluated through logistic regression analysis, receiver operator characteristic (ROC) analysis, integrated discrimination improvement (IDI), and net reclassification improvement (NRI). Functional enrichment analyses were performed to predict the possible mechanisms of circRNAs in CAD. RESULTS A total of ten CAD-related hub circRNAs were identified through WGCNA and LASSO analysis. Among them, hsa_circ_0069972 and hsa_circ_0021509 were highly expressed in blood samples of CAD patients, and they were identified as independent predictors after adjustment for relevant confounders. The area under the ROC curve for hsa_circ_0069972 and hsa_circ_0021509 was 0.760 and 0.717, respectively. The classification of patients was improved with the incorporation of circRNAs into the clinical model composed of conventional cardiovascular risk factors, showing an IDI of 0.131 and NRI of 0.170 for hsa_circ_0069972, and an IDI of 0.111 and NRI of 0.150 for hsa_circ_0021509. Functional enrichment analyses revealed that the hsa_circ_0069972-miRNA-mRNA network was enriched in TGF-β、FoxO and Hippo signaling pathways, while the hsa_circ_0021509-miRNA-mRNA network was enriched in PI3K/Akt and MAPK signaling pathways. CONCLUSION Hsa_circ_0069972 and hsa_circ_0021509 were identified by integrated analysis, and they are highly expressed in CAD patients. They may serve as novel biomarkers for CAD.
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Affiliation(s)
- Qilong Zhong
- General Practice Department, The Seventh Hospital of Ningbo, Ningbo, Zhejiang, China
- Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang, China
| | - Shaoyue Jin
- School of Public Health, Health Science Center, Ningbo University, Ningbo, Zhejiang, China
| | - Zebo Zhang
- School of Public Health, Health Science Center, Ningbo University, Ningbo, Zhejiang, China
- Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Haiyan Qian
- School of Public Health, Health Science Center, Ningbo University, Ningbo, Zhejiang, China
| | - Yanqing Xie
- Institute of Geriatrics, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Peiling Yan
- General Practice Department, The Seventh Hospital of Ningbo, Ningbo, Zhejiang, China
| | - Wenming He
- Institute of Geriatrics, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China.
| | - Lina Zhang
- Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang, China.
- School of Public Health, Health Science Center, Ningbo University, Ningbo, Zhejiang, China.
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19
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Hou C, Liu J, Liu J, Yao D, Liang F, Qin C, Ma Z. METTL3-induced circ_0008345 contributes to the progression of colorectal cancer via the microRNA-182-5p/CYP1A2 pathway. BMC Cancer 2024; 24:728. [PMID: 38877514 PMCID: PMC11177402 DOI: 10.1186/s12885-024-12474-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 06/04/2024] [Indexed: 06/16/2024] Open
Abstract
BACKGROUND Circular RNA (circRNAs) have been found to play major roles in the progression of colorectal cancer (CRC). However, the functions of circ_0008345 (transcribed by PTK2) in regulating CRC development remain undefined. In this study, we aimed to explore the roles and underlying mechanisms of circ_0008345 in CRC. METHODS RNase R-treated total cellular RNA was used to verify the circular structure of circ_0008345, and a subcellular fractionation assay was performed to detect the subcellular localization of circ_0008345. RNA pull-down and dual-luciferase assays were used to verify the binding relation between microRNA (miR)-182-5p and circ_0008345 and/or CYP1A2. Colony formation assay, EdU, and Transwell assays were performed to detect the biological behavior of CRC cells in vitro, and CRC cells were injected into mice to observe the tumor formation. m6A immunoprecipitation was used to detect the m6A modification of circ_0008345 in CRC cells. RESULTS Circ_0008345, upregulated in CRC tissues and cells, was mainly present in the cytoplasm. Circ_0008345 bound to miR-182-5p, and miR-182-5p targeted CYP1A2, an oncogene in CRC. The colony formation, mobility, EdU-positive cell rate in vitro, and tumor growth in mice were inhibited after the knockdown of circ_0008345. However, the suppressing effects of sh-circ_0008345 on CRC and CYP1A2 expression were significantly reversed after further knockdown of miR-182-5p. METTL3 was the m6A modifier mediating circ_0008345 expression, and the suppression of METTL3 reduced the expression of circ_0008345. CONCLUSIONS METTL3-dependent m6A methylation upregulated circ_0008345, which blocked the inhibitory effect of miR-182-5p on CYP1A2, thereby exacerbating the malignant phenotype of CRC cells.
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Affiliation(s)
- Chaofeng Hou
- Department of Anorectal Surgery, Zhengzhou Central Hospital Affiliated to Zhengzhou University, No. 195, Tongbai North Road, Zhongyuan District, Zhengzhou, Henan, 450000, P.R. China
| | - Jinbo Liu
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, P.R. China
| | - Junwei Liu
- Department of Anorectal Surgery, Zhengzhou Central Hospital Affiliated to Zhengzhou University, No. 195, Tongbai North Road, Zhongyuan District, Zhengzhou, Henan, 450000, P.R. China
| | - Danjie Yao
- Department of Anorectal Surgery, Zhengzhou Central Hospital Affiliated to Zhengzhou University, No. 195, Tongbai North Road, Zhongyuan District, Zhengzhou, Henan, 450000, P.R. China
| | - Fang Liang
- Department of Oncology Rehabilitation, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan, 450000, P.R. China
| | - Congpeng Qin
- Department of Anorectal Surgery, Zhengzhou Central Hospital Affiliated to Zhengzhou University, No. 195, Tongbai North Road, Zhongyuan District, Zhengzhou, Henan, 450000, P.R. China
| | - Zhiyong Ma
- Department of Anorectal Surgery, Zhengzhou Central Hospital Affiliated to Zhengzhou University, No. 195, Tongbai North Road, Zhongyuan District, Zhengzhou, Henan, 450000, P.R. China.
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20
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Ma Q, Yu W, Li Z, Zhang X, Zhang L. Circ_0081723 enhances cervical cancer progression and modulates CREBRF via sponging miR-545-3p. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024:10.1007/s00210-024-03175-8. [PMID: 38850307 DOI: 10.1007/s00210-024-03175-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 05/21/2024] [Indexed: 06/10/2024]
Abstract
Circular RNAs (circRNAs) have been confirmed to be an important modulator and therapeutic target of cervical cancer (CC). The aim of this study is to explore the role and mechanism of circ_0081723 in CC progression. Circ_0081723, microRNA-545-3p (miR-545-3p), and CREB3 regulatory factor (CREBRF) levels were detected using quantitative real-time PCR (qRT-PCR) assay. CREBRF, ki-67, Bcl-2 related X protein (Bax), and E-cadherin expression levels were determined using western blot (WB) and immunohistochemistry (IHC) assays. Cell proliferation was assessed using Cell Counting Kit-8 (CCK-8), cell colony formation, and 5-ethynyl-2'-deoxyuridine (EdU) assays. Flow cytometry was used to measure cell apoptosis. Cell migration and invasion were examined using Transwell assay. Interaction between miR-545-3p and circ_0081723 or CREBRF was verified using dual-luciferase reporter assay and RNA immunoprecipitation (RIP) assays. The biological role of circ_0081723 on CC growth was examined using the xenograft tumor model in vivo. Circ_0081723 and CREBRF were increased, and miR-545-3p was decreased in CC tissues and cells. Circ_0081723 silencing suppressed CC cell growth and motility whereas boosted CC cell apoptosis. Besides, circ_0081723 acted as a molecular sponge for miR-545-3p, and circ_0081723 knockdown-induced effects were largely reversed by miR-545-3p downregulation in CC cells. Moreover, miR-545-3p repressed CC progression by targeting CREBRF. Circ_0081723 absence blocked xenograft tumor growth in vivo. Circ_0081723 stimulated CC cell malignant behaviors by regulating the miR-545-3p/CREBRF pathway, providing a possible circRNA-targeted therapy for CC.
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Affiliation(s)
- Qiongyan Ma
- Department of Gynaecology and Obstetrics, Gongli Hospital of Shanghai Pudong New Area, Shanghai, China
| | - Weiwei Yu
- Department of Radiation Oncology, Affiliated Hospital of Nantong University, Nantong, China
| | - Zhaobin Li
- Department of Radiation Oncology, Shanghai Sixth People's Hospital, Shanghai Jiaotong University School of Medicine, No. 600, Yishan Road, Xuhui District, Shanghai, 200233, China
| | - Xiulong Zhang
- Department of Radiation Oncology, Shanghai Sixth People's Hospital, Shanghai Jiaotong University School of Medicine, No. 600, Yishan Road, Xuhui District, Shanghai, 200233, China
| | - Lihua Zhang
- Department of Radiation Oncology, Shanghai Sixth People's Hospital, Shanghai Jiaotong University School of Medicine, No. 600, Yishan Road, Xuhui District, Shanghai, 200233, China.
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21
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Lin JJ, Chen R, Yang LY, Gong M, Du MY, Mu SQ, Jiang ZA, Li HH, Yang Y, Wang XH, Wang SF, Liu KX, Cao SH, Wang ZY, Zhao AQ, Yang SY, Li C, Sun SG. Hsa_circ_0001402 alleviates vascular neointimal hyperplasia through a miR-183-5p-dependent regulation of vascular smooth muscle cell proliferation, migration, and autophagy. J Adv Res 2024; 60:93-110. [PMID: 37499939 PMCID: PMC11156604 DOI: 10.1016/j.jare.2023.07.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 07/14/2023] [Accepted: 07/24/2023] [Indexed: 07/29/2023] Open
Abstract
INTRODUCTION Vascular neointimal hyperplasia, a pathological process observed in cardiovascular diseases such as atherosclerosis and pulmonary hypertension, involves the abundant presence of vascular smooth muscle cells (VSMCs). The proliferation, migration, and autophagy of VSMCs are associated with the development of neointimal lesions. Circular RNAs (circRNAs) play critical roles in regulating VSMC proliferation and migration, thereby participating in neointimal hyperplasia. However, the regulatory roles of circRNAs in VSMC autophagy remain unclear. OBJECTIVES We aimed to identify circRNAs that are involved in VSMC autophagy-mediated neointimal hyperplasia, as well as elucidate the underlying mechanisms. METHODS Dual-luciferase reporter gene assay was performed to validate two competing endogenous RNA axes, hsa_circ_0001402/miR-183-5p/FKBP prolyl isomerase like (FKBPL) and hsa_circ_0001402/miR-183-5p/beclin 1 (BECN1). Cell proliferation and migration analyses were employed to investigate the effects of hsa_circ_0001402, miR-183-5p, or FKBPL on VSMC proliferation and migration. Cell autophagy analysis was conducted to reveal the role of hsa_circ_0001402 or miR-183-5p on VSMC autophagy. The role of hsa_circ_0001402 or miR-183-5p on neointimal hyperplasia was evaluated using a mouse model of common carotid artery ligation. RESULTS Hsa_circ_0001402 acted as a sponge for miR-183-5p, leading to the suppression of miR-183-5p expression. Through direct interaction with the coding sequence (CDS) of FKBPL, miR-183-5p promoted VSMC proliferation and migration by decreasing FKBPL levels. Besides, miR-183-5p reduced BECN1 levels by targeting the 3'-untranslated region (UTR) of BECN1, thus inhibiting VSMC autophagy. By acting as a miR-183-5p sponge, overexpression of hsa_circ_0001402 increased FKBPL levels to inhibit VSMC proliferation and migration, while simultaneously elevating BECN1 levels to activate VSMC autophagy, thereby alleviating neointimal hyperplasia. CONCLUSION Hsa_circ_0001402, acting as a miR-183-5p sponge, increases FKBPL levels to inhibit VSMC proliferation and migration, while enhancing BECN1 levels to activate VSMC autophagy, thus alleviating neointimal hyperplasia. The hsa_circ_0001402/miR-183-5p/FKBPL axis and hsa_circ_0001402/miR-183-5p/BECN1 axis may offer potential therapeutic targets for neointimal hyperplasia.
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Affiliation(s)
- Jia-Jie Lin
- Department of Biochemistry and Molecular Biology, Key Laboratory of Medical Biotechnology of Hebei Province, Cardiovascular Medical Science Center, Hebei Medical University, Shijiazhuang 050017, China
| | - Rui Chen
- Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Li-Yun Yang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Medical Biotechnology of Hebei Province, Cardiovascular Medical Science Center, Hebei Medical University, Shijiazhuang 050017, China
| | - Miao Gong
- Department of Biochemistry and Molecular Biology, Key Laboratory of Medical Biotechnology of Hebei Province, Cardiovascular Medical Science Center, Hebei Medical University, Shijiazhuang 050017, China
| | - Mei-Yang Du
- Department of Biochemistry and Molecular Biology, Key Laboratory of Medical Biotechnology of Hebei Province, Cardiovascular Medical Science Center, Hebei Medical University, Shijiazhuang 050017, China
| | - Shi-Qing Mu
- Department of Biochemistry and Molecular Biology, Key Laboratory of Medical Biotechnology of Hebei Province, Cardiovascular Medical Science Center, Hebei Medical University, Shijiazhuang 050017, China
| | - Ze-An Jiang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Medical Biotechnology of Hebei Province, Cardiovascular Medical Science Center, Hebei Medical University, Shijiazhuang 050017, China
| | - Huan-Huan Li
- Department of Biochemistry and Molecular Biology, Key Laboratory of Medical Biotechnology of Hebei Province, Cardiovascular Medical Science Center, Hebei Medical University, Shijiazhuang 050017, China
| | - Yang Yang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Medical Biotechnology of Hebei Province, Cardiovascular Medical Science Center, Hebei Medical University, Shijiazhuang 050017, China
| | - Xing-Hui Wang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Medical Biotechnology of Hebei Province, Cardiovascular Medical Science Center, Hebei Medical University, Shijiazhuang 050017, China
| | - Si-Fan Wang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Medical Biotechnology of Hebei Province, Cardiovascular Medical Science Center, Hebei Medical University, Shijiazhuang 050017, China
| | - Ke-Xin Liu
- Department of Biochemistry and Molecular Biology, Key Laboratory of Medical Biotechnology of Hebei Province, Cardiovascular Medical Science Center, Hebei Medical University, Shijiazhuang 050017, China
| | - Shan-Hu Cao
- Department of Biochemistry and Molecular Biology, Key Laboratory of Medical Biotechnology of Hebei Province, Cardiovascular Medical Science Center, Hebei Medical University, Shijiazhuang 050017, China
| | - Zhao-Yi Wang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Medical Biotechnology of Hebei Province, Cardiovascular Medical Science Center, Hebei Medical University, Shijiazhuang 050017, China
| | - An-Qi Zhao
- Department of Biochemistry and Molecular Biology, Key Laboratory of Medical Biotechnology of Hebei Province, Cardiovascular Medical Science Center, Hebei Medical University, Shijiazhuang 050017, China
| | - Shu-Yan Yang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing 100020, China.
| | - Cheng Li
- Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute, Guangdong Second Provincial General Hospital, Guangzhou 510317, China.
| | - Shao-Guang Sun
- Department of Biochemistry and Molecular Biology, Key Laboratory of Medical Biotechnology of Hebei Province, Cardiovascular Medical Science Center, Hebei Medical University, Shijiazhuang 050017, China.
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22
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Digby B, Finn S, Ó Broin P. Computational approaches and challenges in the analysis of circRNA data. BMC Genomics 2024; 25:527. [PMID: 38807085 PMCID: PMC11134749 DOI: 10.1186/s12864-024-10420-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 05/15/2024] [Indexed: 05/30/2024] Open
Abstract
Circular RNAs (circRNA) are a class of non-coding RNA, forming a single-stranded covalently closed loop structure generated via back-splicing. Advancements in sequencing methods and technologies in conjunction with algorithmic developments of bioinformatics tools have enabled researchers to characterise the origin and function of circRNAs, with practical applications as a biomarker of diseases becoming increasingly relevant. Computational methods developed for circRNA analysis are predicated on detecting the chimeric back-splice junction of circRNAs whilst mitigating false-positive sequencing artefacts. In this review, we discuss in detail the computational strategies developed for circRNA identification, highlighting a selection of tool strengths, weaknesses and assumptions. In addition to circRNA identification tools, we describe methods for characterising the role of circRNAs within the competing endogenous RNA (ceRNA) network, their interactions with RNA-binding proteins, and publicly available databases for rich circRNA annotation.
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Affiliation(s)
- Barry Digby
- School of Mathematical and Statistical Sciences, University of Galway, Galway, Ireland.
| | - Stephen Finn
- Discipline of Histopathology, School of Medicine, Trinity College Dublin and Cancer Molecular Diagnostic Laboratory, Dublin, Ireland
| | - Pilib Ó Broin
- School of Mathematical and Statistical Sciences, University of Galway, Galway, Ireland
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23
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Li Y, Wang Z, Yang J, Sun Y, He Y, Wang Y, Chen X, Liang Y, Zhang N, Wang X, Zhao W, Hu G, Yang Q. CircTRIM1 encodes TRIM1-269aa to promote chemoresistance and metastasis of TNBC via enhancing CaM-dependent MARCKS translocation and PI3K/AKT/mTOR activation. Mol Cancer 2024; 23:102. [PMID: 38755678 PMCID: PMC11097450 DOI: 10.1186/s12943-024-02019-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024] Open
Abstract
Peptides and proteins encoded by noncanonical open reading frames (ORFs) of circRNAs have recently been recognized to play important roles in disease progression, but the biological functions and mechanisms of these peptides and proteins are largely unknown. Here, we identified a potential coding circular RNA, circTRIM1, that was upregulated in doxorubicin-resistant TNBC cells by intersecting transcriptome and translatome RNA-seq data, and its expression was correlated with clinicopathological characteristics and poor prognosis in patients with TNBC. CircTRIM1 possesses a functional IRES element along with an 810 nt ORF that can be translated into a novel endogenously expressed protein termed TRIM1-269aa. Functionally, we demonstrated that TRIM1-269aa, which is involved in the biological functions of circTRIM1, promoted chemoresistance and metastasis in TNBC cells both in vitro and in vivo. In addition, we found that TRIM1-269aa can be packaged into exosomes and transmitted between TNBC cells. Mechanistically, TRIM1-269aa enhanced the interaction between MARCKS and calmodulin, thus promoting the calmodulin-dependent translocation of MARCKS, which further initiated the activation of the PI3K/AKT/mTOR pathway. Overall, circTRIM1, which encodes TRIM1-269aa, promoted TNBC chemoresistance and metastasis by enhancing MARCKS translocation and PI3K/AKT/mTOR activation. Our investigation has yielded novel insights into the roles of protein-coding circRNAs and supported circTRIM1/TRIM1-269aa as a novel promising prognostic and therapeutic target for patients with TNBC.
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Affiliation(s)
- Yaming Li
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Zekun Wang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Jingwen Yang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Yuhan Sun
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Yinqiao He
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Yuping Wang
- School of Basic Medicine, Jining Medical College, Jining, Shandong, 272067, China
| | - Xi Chen
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Yiran Liang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Ning Zhang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Xiaolong Wang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Wenjing Zhao
- Pathology Tissue Bank, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Guohong Hu
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Qifeng Yang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China.
- Pathology Tissue Bank, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China.
- Research Institute of Breast Cancer, Shandong University, Jinan, Shandong, 250012, China.
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24
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Yang J, Wei Z, Li H, Lv S, Fu Y, Xiao L. Paeoniflorin inhibits the inflammation of rheumatoid arthritis fibroblast-like synoviocytes by downregulating hsa_circ_009012. Heliyon 2024; 10:e30555. [PMID: 38726183 PMCID: PMC11079323 DOI: 10.1016/j.heliyon.2024.e30555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
Background Rheumatoid arthritis (RA) is a chronic inflammatory disease that leads to progressive joint damage. Circular RNA (circRNA) can regulate the inflammatory response of fibroblast-like synoviocytes (FLSs) in RA, influencing the disease progression. Paeoniflorin (PF) is the main active ingredient extracted from Paeonia lactiflora and is known for its anti-inflammatory effect. This study aims to explore the potential mechanisms by which hsa_circ_009012 and PF regulate the inflammatory response in RA. Methods RNA expression of hsa_circ_009012, has-microRNA-1286 (miR-1286), toll-like receptor 4 (TLR4), NOD-like receptor thermal protein domain associated protein 3 (NLRP3) was assessed by real-time quantitative polymerase chain reaction (RT-qPCR) or western blotting (WB). Cell inflammation markers (TNF-α, IL-1β, IL-6) were assessed by RT-qPCR and immunofluorescence (IF). Counting Kit-8 (CCK-8) assay, flow cytometry, and transwell assay were utilized to test cell viability, cell cycle distribution, and migration. Results Hsa_circ_009012 was highly expressed in RA-FLS. Hsa_circ_009012 over-expression facilitated the inflammation in RA-FLS and was closely associated with the miR-1286/TLR4 axis. Paeoniflorin inhibited inflammation and the expression of hsa_circ_009012 and TLR4, while upregulating the expression of miR-1286 in RA-FLS. Moreover, the upregulation of hsa_circ_009012 reversed the repressive effect of paeoniflorin on RA-FLS progression. Conclusion Paeoniflorin inhibits the inflammation of RA-FLS via mediating the hsa_circ_009012/miR-1286/TLR4/NLRP3 axis.
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Affiliation(s)
- Junping Yang
- Affiliated Hospital of Jiangxi University of Chinese Medicine, Nanchang, 330006, Jiangxi, People's Republic of China
- Jiangxi University of Chinese Medicine, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Zehong Wei
- Jiangxi University of Chinese Medicine, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Huaiyu Li
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510405, Guangdong, People's Republic of China
- Jiangxi University of Chinese Medicine, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Senhao Lv
- Jiangxi University of Chinese Medicine, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Yong Fu
- Affiliated Hospital of Jiangxi University of Chinese Medicine, Nanchang, 330006, Jiangxi, People's Republic of China
- Jiangxi University of Chinese Medicine, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Liang Xiao
- Affiliated Hospital of Jiangxi University of Chinese Medicine, Nanchang, 330006, Jiangxi, People's Republic of China
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25
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Zhao YX, Yu CQ, Li LP, Wang DW, Song HF, Wei Y. BJLD-CMI: a predictive circRNA-miRNA interactions model combining multi-angle feature information. Front Genet 2024; 15:1399810. [PMID: 38798699 PMCID: PMC11116695 DOI: 10.3389/fgene.2024.1399810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 04/03/2024] [Indexed: 05/29/2024] Open
Abstract
Increasing research findings suggest that circular RNA (circRNA) exerts a crucial function in the pathogenesis of complex human diseases by binding to miRNA. Identifying their potential interactions is of paramount importance for the diagnosis and treatment of diseases. However, long cycles, small scales, and time-consuming processes characterize previous biological wet experiments. Consequently, the use of an efficient computational model to forecast the interactions between circRNA and miRNA is gradually becoming mainstream. In this study, we present a new prediction model named BJLD-CMI. The model extracts circRNA sequence features and miRNA sequence features by applying Jaccard and Bert's method and organically integrates them to obtain CMI attribute features, and then uses the graph embedding method Line to extract CMI behavioral features based on the known circRNA-miRNA correlation graph information. And then we predict the potential circRNA-miRNA interactions by fusing the multi-angle feature information such as attribute and behavior through Autoencoder in Autoencoder Networks. BJLD-CMI attained 94.95% and 90.69% of the area under the ROC curve on the CMI-9589 and CMI-9905 datasets. When compared with existing models, the results indicate that BJLD-CMI exhibits the best overall competence. During the case study experiment, we conducted a PubMed literature search to confirm that out of the top 10 predicted CMIs, seven pairs did indeed exist. These results suggest that BJLD-CMI is an effective method for predicting interactions between circRNAs and miRNAs. It provides a valuable candidate for biological wet experiments and can reduce the burden of researchers.
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Affiliation(s)
- Yi-Xin Zhao
- School of information Engineering, Xijing University, Xi’an, China
| | - Chang-Qing Yu
- School of information Engineering, Xijing University, Xi’an, China
| | - Li-Ping Li
- School of information Engineering, Xijing University, Xi’an, China
- College of Grassland and Environment Sciences, Xinjiang Agricultural University, Ürümqi, China
| | - Deng-Wu Wang
- School of information Engineering, Xijing University, Xi’an, China
| | - Hui-Fan Song
- School of information Engineering, Xijing University, Xi’an, China
| | - Yu Wei
- School of information Engineering, Xijing University, Xi’an, China
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26
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Torshizi Esfahani A, Mohammadpour S, Jalali P, Yaghoobi A, Karimpour R, Torkamani S, Pardakhtchi A, Salehi Z, Nazemalhosseini-Mojarad E. Differential expression of angiogenesis-related genes 'VEGF' and 'angiopoietin-1' in metastatic and EMAST-positive colorectal cancer patients. Sci Rep 2024; 14:10539. [PMID: 38719941 PMCID: PMC11079037 DOI: 10.1038/s41598-024-61000-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
Abnormal angiogenesis leads to tumor progression and metastasis in colorectal cancer (CRC). This study aimed to elucidate the association between angiogenesis-related genes, including VEGF-A, ANGPT-1, and ANGPT-2 with both metastatic and microsatellite alterations at selected tetranucleotide repeats (EMAST) subtypes of CRC. We conducted a thorough assessment of the ANGPT-1, ANGPT-2, and VEGF-A gene expression utilizing publicly available RNA sequencing and microarray datasets. Then, the experimental validation was performed in 122 CRC patients, considering their disease metastasis and EMAST+/- profile by using reverse transcription polymerase chain reaction (RT-PCR). Subsequently, a competing endogenous RNA (ceRNA) network associated with these angiogenesis-related genes was constructed and analyzed. The expression level of VEGF-A and ANGPT-2 genes were significantly higher in tumor tissues as compared with normal adjacent tissues (P-value < 0.001). Nevertheless, ANGPT-1 had a significantly lower expression in tumor samples than in normal colon tissue (P-value < 0.01). We identified a significantly increased VEGF-A (P-value = 0.002) and decreased ANGPT-1 (P-value = 0.04) expression in EMAST+ colorectal tumors. Regarding metastasis, a significantly increased VEGF-A and ANGPT-2 expression (P-value = 0.001) and decreased ANGPT-1 expression (P-value < 0.05) were established in metastatic CRC patients. Remarkably, co-expression analysis also showed a strong correlation between ANGPT-2 and VEGF-A gene expressions. The ceRNA network was constructed by ANGPT-1, ANGPT-2, VEGF-A, and experimentally validated miRNAs (hsa-miR-190a-3p, hsa-miR-374c-5p, hsa-miR-452-5p, and hsa-miR-889-3p), lncRNAs (AFAP1-AS1, KCNQ1OT1 and MALAT1), and TFs (Sp1, E2F1, and STAT3). Network analysis revealed that colorectal cancer is amongst the 82 significant pathways. We demonstrated a significant differential expression of VEGF-A and ANGPT-1 in colorectal cancer patients exhibiting the EMAST+ phenotype. This finding provides novel insights into the molecular pathogenesis of colorectal cancer, specifically in EMAST subtypes. Yet, the generalization of in silico findings to EMAST+ colorectal cancer warrants future experimental investigations. In the end, this study proposes that the EMAST biomarker could serve as an additional perspective on CMS4 biology which is well-defined by activated angiogenesis and worse overall survival.
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Affiliation(s)
- Amir Torshizi Esfahani
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Somayeh Mohammadpour
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Pooya Jalali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Yaghoobi
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Raana Karimpour
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Soha Torkamani
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ali Pardakhtchi
- Department of Cellular and Molecular Biology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Zahra Salehi
- Hematology, Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical Sciences, Tehran, Iran.
- Research Institute for Oncology, Hematology and Cell Therapy, Tehran University of Medical Sciences, Tehran, Iran.
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
- Department of Surgery, Leiden University Medical Center, Leiden, Netherlands.
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27
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Chen Z, Ma X, Chen Z, Chen W, Li L, Lin Y, Hu Y, Shang Y, Zhao Y, He J, Zhou C, Meng X. Exosome-transported circ_0061407 and circ_0008103 play a tumour-repressive role and show diagnostic value in non-small-cell lung cancer. J Transl Med 2024; 22:427. [PMID: 38711144 DOI: 10.1186/s12967-024-05215-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 04/16/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND Circular RNAs (circRNAs), one of the major contents of exosomes, have been shown to participate in the occurrence and progression of cancers. The role and the diagnostic potential of exosome-transported circRNAs in non-small-cell lung cancer (NSCLC) remain largely unknown. METHODS The NSCLC-associated exosomal circ_0061407 and circ_0008103 were screened by circRNA microarray. The role of circ_0061407 and circ_0008103 in NSCLC was examined in vitro and in vivo. The encapsulation of the two circRNAs into exosomes and the transport to recipient cells were observed by confocal microscopy. The effects of exosome-transported circ_0061407 and circ_0008103 on recipient cells were investigated using a co-culture device. Bioinformatics analyses were performed to predict the mechanisms by which circ_0061407 and circ_0008103 affected NSCLC. The quantitative polymerase chain reaction was used to quantify the exosome-containing circ_0061407 and circ_0008103 in the serum samples of healthy, pneumonia, benign lung tumours, and NSCLC. The diagnostic efficacy was evaluated using receiver operating characteristic curves. RESULTS The levels of circ_0061407 and circ_0008103 within exosomes were down-regulated in the serum of patients with NSCLC. The up-regulation of circ_0061407 and circ_0008103 inhibited the proliferation, migration/invasion, cloning formation of NSCLC cells in vitro and inhibited lung tumour growth in vivo. Circ_0061407 and circ_0008103 were observed to be packaged in exosomes and transported to recipient cells, where they inhibited the proliferation, migration/invasion, and cloning formation abilities of the recipient cells. Moreover, circ_0061407 and circ_0008103 might be involved in the progression of NSCLC by interacting with microRNAs and proteins. Additionally, lower serum exosomal circ_0061407 and circ_0008103 levels were associated with advanced pathological staging and distant metastasis. CONCLUSIONS This study identified two novel exosome-transported circRNAs (circ_0061407 and circ_0008103) associated with NSCLC. These findings may provide additional insights into the development of NSCLC and potential diagnostic biomarkers for NSCLC.
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MESH Headings
- Exosomes/metabolism
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Non-Small-Cell Lung/blood
- RNA, Circular/genetics
- RNA, Circular/blood
- RNA, Circular/metabolism
- Humans
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Lung Neoplasms/blood
- Animals
- Cell Line, Tumor
- Cell Movement/genetics
- Cell Proliferation/genetics
- Male
- Gene Expression Regulation, Neoplastic
- Female
- Mice, Nude
- Middle Aged
- Mice, Inbred BALB C
- ROC Curve
- Mice
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Affiliation(s)
- Zhenhua Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Xinyi Ma
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Ziyuan Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, 315020, Zhejiang, China
| | - Wei Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, 315020, Zhejiang, China
| | - Leyi Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Yichen Lin
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Yulin Hu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Yue Shang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Yikai Zhao
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Jinxian He
- Department of Thoracic Surgery, The Ningbo Medical Center Lihuili Hospital, Ningbo University, Ningbo, 315048, China
| | - Chengwei Zhou
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, Ningbo, 315020, Zhejiang, China
| | - Xiaodan Meng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Health Science Center, Ningbo University, 818 Fenghua Road, Ningbo, 315211, Zhejiang, China.
- Zhejiang Provincial Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China.
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Lu F, Mo L, Liu A. Circ_0001360 absence alleviates oxygen-glucose deprivation/reoxygenation-induced SK-N-SH cell injury via controlling the miR-671-5p/BMF pathway. Int J Neurosci 2024; 134:492-502. [PMID: 36039693 DOI: 10.1080/00207454.2022.2118598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/27/2022] [Accepted: 08/22/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND The regulatory potency of circular RNA (circRNA) has been acknowledged in multiple human diseases, including ischaemic stroke (IS). However, only a few circRNAs were investigated in this disorder. We aimed to uncover the role of circ_0001360 in cell models of IS in vitro. METHODS SK-N-SH cells were subjected to oxygen-glucose deprivation/reoxygenation (OGD/R) to simulate IS pathology conditions in vitro. Quantitative real-time PCR (qPCR) and western blot were applied for expression detection. Cell viability, proliferation and apoptosis were investigated by CCK-8, EdU and flow cytometry assays. The predicted binding of miR-671-5p to circ_0001360 or BMF 3'UTR was validated by dual-luciferase reporter and RIP assays. Proteins on the NF-κB pathway were quantified by western blot to assess NF-κB pathway activity. RESULTS Circ_0001360 was upregulated in SK-N-SH cells after OGD/R treatment. OGD/R provoked SK-N-SH cell growth impairment, apoptosis and inflammation, while circ_0001360 knockdown relieved these injuries. Circ_0001360 targeted miR-671-5p, and miR-671-5p deficiency recovered SK-N-SH cell injury that was repressed by circ_0001360 knockdown. MiR-671-5p directly combined with BMF and repressed BMF expression. Accordingly, circ_0001360 targeted miR-671-5p to regulate the expression of BMF. Circ_0001360 knockdown weakened the phosphorylated levels of P65 and IκBα, while further miR-671-5p deficiency or BMF overexpression restored their expression levels. CONCLUSION Circ_0001360 contributed to OGD/R-caused SK-N-SH cell injury via targeting the miR-671-5p/BMF network and activating the NF-κB pathway, thus participating in the development of IS.
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Affiliation(s)
- Fang Lu
- Department of Neurology, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China
| | - Linhong Mo
- Department of Neurology, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China
| | - Aixian Liu
- Department of Neurology, Beijing Rehabilitation Hospital, Capital Medical University, Beijing, China
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29
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Drula R, Braicu C, Neagoe IB. Current advances in circular RNA detection and investigation methods: Are we running in circles? WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1850. [PMID: 38702943 DOI: 10.1002/wrna.1850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/30/2024] [Accepted: 04/01/2024] [Indexed: 05/06/2024]
Abstract
Circular RNAs (circRNAs), characterized by their closed-loop structure, have emerged as significant transcriptomic regulators, with roles spanning from microRNA sponging to modulation of gene expression and potential peptide coding. The discovery and functional analysis of circRNAs have been propelled by advancements in both experimental and bioinformatics tools, yet the field grapples with challenges related to their detection, isoform diversity, and accurate quantification. This review navigates through the evolution of circRNA research methodologies, from early detection techniques to current state-of-the-art approaches that offer comprehensive insights into circRNA biology. We examine the limitations of existing methods, particularly the difficulty in differentiating circRNA isoforms and distinguishing circRNAs from their linear counterparts. A critical evaluation of various bioinformatics tools and novel experimental strategies is presented, emphasizing the need for integrated approaches to enhance our understanding and interpretation of circRNA functions. Our insights underscore the dynamic and rapidly advancing nature of circRNA research, highlighting the ongoing development of analytical frameworks designed to address the complexity of circRNAs and facilitate the assessment of their clinical utility. As such, this comprehensive overview aims to catalyze further advancements in circRNA study, fostering a deeper understanding of their roles in cellular processes and potential implications in disease. This article is categorized under: RNA Methods > RNA Nanotechnology RNA Methods > RNA Analyses in Cells RNA Methods > RNA Analyses In Vitro and In Silico.
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Affiliation(s)
- Rareș Drula
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ioana-Berindan Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
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30
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Ruan D, Xu J, Liu Y, Luo J, Zhao X, Li Y, Wang G, Feng J, Liang H, Yin Y, Luo J, Yin Y. CircPTEN-MT from PTEN regulates mitochondrial energy metabolism. J Genet Genomics 2024; 51:531-542. [PMID: 38184105 DOI: 10.1016/j.jgg.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/08/2024]
Abstract
Phosphatase and tensin homolog (PTEN) is a multifunctional gene involved in a variety of physiological and pathological processes. Circular RNAs (circRNAs) are generated from back-splicing events during mRNA processing and participate in cell biological processes through binding to RNAs or proteins. However, PTEN-related circRNAs are largely unknown. Here, we report that circPTEN- mitochondria (MT) (hsa_circ_0002934) is a circular RNA encoded by exons 3, 4, and 5 of PTEN and is a critical regulator of mitochondrial energy metabolism. CircPTEN-MT is localized to mitochondria and physically associated with leucine-rich pentatricopeptide repeat-containing protein (LRPPRC), which regulates posttranscriptional gene expression in mitochondria. Knocking down circPTEN-MT reduces the interaction of LRPPRC and steroid receptor RNA activator (SRA) stem-loop interacting RNA binding protein (SLIRP) and inhibits the polyadenylation of mitochondrial mRNA, which decreases the mRNA level of the mitochondrial complex I subunit and reduces mitochondrial membrane potential and adenosine triphosphate production. Our data demonstrate that circPTEN-MT is an important regulator of cellular energy metabolism. This study expands our understanding of the role of PTEN, which produces both linear and circular RNAs with different and independent functions.
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Affiliation(s)
- Danhui Ruan
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University International Cancer Institute, Peking-Tsinghua Center of Life Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jiancheng Xu
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University International Cancer Institute, Peking-Tsinghua Center of Life Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yang Liu
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University International Cancer Institute, Peking-Tsinghua Center of Life Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Juan Luo
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, China
| | - Xuyang Zhao
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University International Cancer Institute, Peking-Tsinghua Center of Life Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yuhua Li
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University International Cancer Institute, Peking-Tsinghua Center of Life Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Guangxi Wang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University International Cancer Institute, Peking-Tsinghua Center of Life Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jiawen Feng
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University International Cancer Institute, Peking-Tsinghua Center of Life Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Hui Liang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University International Cancer Institute, Peking-Tsinghua Center of Life Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yue Yin
- Department of Pharmacology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jianyuan Luo
- Department of Medical Genetics, Center for Medical Genetics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yuxin Yin
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University International Cancer Institute, Peking-Tsinghua Center of Life Sciences, Peking University Health Science Center, Beijing 100191, China; Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, Guangdong 518036, China.
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31
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Chen H, Wen J, Zhang W, Ma W, Guo Y, Shen L, Zhang Z, Yang F, Zhang Y, Gao Y, Xu T, Yan Y, Li W, Zhang J, Mao S, Yao X. circKDM1A suppresses bladder cancer progression by sponging miR-889-3p/CPEB3 and stabilizing p53 mRNA. iScience 2024; 27:109624. [PMID: 38632984 PMCID: PMC11022052 DOI: 10.1016/j.isci.2024.109624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/04/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
Circular RNAs (circRNAs) play crucial biological functions in various tumors, including bladder cancer (BCa). However, the roles and underlying molecular mechanisms of circRNAs in the malignant proliferation of BCa are yet unknown. CircKDM1A was observed to be downregulated in BCa tissues and cells. Knockdown of circKDM1A promoted the proliferation of BCa cells and bladder xenograft growth, while the overexpression of circKDM1A exerts the opposite effect. The dual-luciferase reporter assay revealed that circKDM1A was directly bound to miR-889-3p, acting as its molecular sponge to downregulate CPEB3. In turn, the CPEB3 was bound to the CPE signal in p53 mRNA 3'UTR to stabilize its expression. Thus, circKDM1A-mediated CPEB3 downregulation inhibits the stability of p53 mRNA and promotes BCa malignant progression. In conclusion, circKDM1A functions as a tumor suppressor in the malignant proliferation of BCa via the miR-889-3p/CPEB3/p53 axis. CircKDM1A may be a potential prognostic biomarker and therapeutic target of BCa.
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Affiliation(s)
- Haotian Chen
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Jing Wen
- Institute of Energy Metabolism and Health, Shanghai Tenth People’s Hospital, Tongji University School of Medicine Shanghai, Shanghai 200072, P.R. China
| | - Wentao Zhang
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Wenchao Ma
- Department of Reproduction, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Yadong Guo
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Liliang Shen
- Department of Urology, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
| | - Zhijin Zhang
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Fuhan Yang
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Yue Zhang
- Department of Central Laboratory, Clinical Medicine Scientific and Technical Innovation Park, Shanghai Tenth People’s Hospital, Shanghai 200435, China
| | - Yaohui Gao
- Department of Pathology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Tianyuan Xu
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Yang Yan
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Wei Li
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Junfeng Zhang
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Shiyu Mao
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
| | - Xudong Yao
- Department of Urology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
- Urologic Cancer Institute, School of Medicine, Tongji University, Shanghai, China
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Guo Y, Huang C, Qiu L, Fu J, Xu C, Yang F. CircTHBS1 promotes trophoblast cell migration and invasion and inhibits trophoblast apoptosis by regulating miR-136-3p/IGF2R axis. FASEB J 2024; 38:e23598. [PMID: 38581244 DOI: 10.1096/fj.202302113rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 03/16/2024] [Accepted: 03/25/2024] [Indexed: 04/08/2024]
Abstract
The precise molecular mechanism behind fetal growth restriction (FGR) is still unclear, although there is a strong connection between placental dysfunction, inadequate trophoblast invasion, and its etiology and pathogenesis. As a new type of non-coding RNA, circRNA has been shown to play a crucial role in the development of FGR. This investigation identified the downregulation of hsa_circ_0034533 (circTHBS1) in FGR placentas through high-sequencing analysis and confirmed this finding in 25 clinical placenta samples using qRT-PCR. Subsequent in vitro functional assays demonstrated that silencing circTHBS1 inhibited trophoblast proliferation, migration, invasion, and epithelial mesenchymal transition (EMT) progression and promoted apoptosis. Furthermore, when circTHBS1 was overexpressed, cell function experiments showed the opposite result. Analysis using fluorescence in situ hybridization revealed that circTHBS1 was primarily found in the cytoplasmic region. Through bioinformatics analysis, we anticipated the involvement of miR-136-3p and IGF2R in downstream processes, which was subsequently validated through qRT-PCR and dual-luciferase assays. Moreover, the inhibition of miR-136-3p or the overexpression of IGF2R partially reinstated proliferation, migration, and invasion abilities following the silencing of circTHBS1. In summary, the circTHBS1/miR-136-3p/IGF2R axis plays a crucial role in the progression and development of FGR, offering potential avenues for the exploration of biological indicators and treatment targets.
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Affiliation(s)
- Yanyan Guo
- Department of Fetal Medicine and Prenatal Diagnosis, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Chuyi Huang
- Department of Fetal Medicine and Prenatal Diagnosis, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Liyan Qiu
- Department of Fetal Medicine and Prenatal Diagnosis, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jiahui Fu
- Department of Fetal Medicine and Prenatal Diagnosis, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Cailing Xu
- Department of Fetal Medicine and Prenatal Diagnosis, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Fang Yang
- Department of Fetal Medicine and Prenatal Diagnosis, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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He S, Lai D, Ma C, Meng C, Cai C, Chen Q, Gu C, Qiu Q. hsa_circ_0087100/hsa-miR-6743-5p affects Th1 cell differentiation by regulating STAT1 in diabetic retinopathy. Epigenomics 2024; 16:427-444. [PMID: 38410923 DOI: 10.2217/epi-2023-0359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024] Open
Abstract
Objective: To elucidate the role of the competitive endogenous RNA (ceRNA) network in immune infiltration of diabetic retinopathy (DR). Methods: We obtained differentially expressed (DE) circRNAs, miRNAs and mRNAs from the Gene Expression Omnibus database. Then, we identified immune infiltration by CIBERSORT and single-sample gene set enrichment analysis and discovered co-expression genes by weighted gene co-expression network analysis. Furthermore, STAT1-mediated Th1 differentiation was determined in DR cell models, DR patients and DR mouse models. Results: hsa_circ_0087100/hsa-miR-6743-5p/STAT1 was involved in immune infiltration of Th1 cells. Aberrant expression of the ceRNA network and STAT1-mediated Th1 differentiation was thus verified in vitro and in vivo. Conclusion: hsa_circ_0087100/hsa-miR-6743-5p/STAT1 may affect Th1 cell differentiation in DR.
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Affiliation(s)
- Shuai He
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
- National Clinical Research Center for Eye Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science & Photomedicine, Shanghai Engineering Center for Precise Diagnosis & Treatment of Eye Diseases, Shanghai, PR China
| | - Dongwei Lai
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
- National Clinical Research Center for Eye Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science & Photomedicine, Shanghai Engineering Center for Precise Diagnosis & Treatment of Eye Diseases, Shanghai, PR China
| | - Chenggong Ma
- Xiangya School of Medicine, Central South University, Changsha, Hunan, PR China
| | - Chunren Meng
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
- National Clinical Research Center for Eye Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science & Photomedicine, Shanghai Engineering Center for Precise Diagnosis & Treatment of Eye Diseases, Shanghai, PR China
| | - Chunyang Cai
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
- National Clinical Research Center for Eye Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science & Photomedicine, Shanghai Engineering Center for Precise Diagnosis & Treatment of Eye Diseases, Shanghai, PR China
| | - Qian Chen
- Department of Ophthalmology, Tong Ren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Chufeng Gu
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
- National Clinical Research Center for Eye Diseases, Shanghai Key Laboratory of Ocular Fundus Diseases, Shanghai Engineering Center for Visual Science & Photomedicine, Shanghai Engineering Center for Precise Diagnosis & Treatment of Eye Diseases, Shanghai, PR China
| | - Qinghua Qiu
- Department of Ophthalmology, Tong Ren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
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Yang J, Lei X, Zhang F. Identification of circRNA-disease associations via multi-model fusion and ensemble learning. J Cell Mol Med 2024; 28:e18180. [PMID: 38506066 PMCID: PMC10951890 DOI: 10.1111/jcmm.18180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/21/2024] [Accepted: 02/05/2024] [Indexed: 03/21/2024] Open
Abstract
Circular RNA (circRNA) is a common non-coding RNA and plays an important role in the diagnosis and therapy of human diseases, circRNA-disease associations prediction based on computational methods can provide a new way for better clinical diagnosis. In this article, we proposed a novel method for circRNA-disease associations prediction based on ensemble learning, named ELCDA. First, the association heterogeneous network was constructed via collecting multiple information of circRNAs and diseases, and multiple similarity measures are adopted here, then, we use metapath, matrix factorization and GraphSAGE-based models to extract features of nodes from different views, the final comprehensive features of circRNAs and diseases via ensemble learning, finally, a soft voting ensemble strategy is used to integrate the predicted results of all classifier. The performance of ELCDA is evaluated by fivefold cross-validation and compare with other state-of-the-art methods, the experimental results show that ELCDA is outperformance than others. Furthermore, three common diseases are used as case studies, which also demonstrate that ELCDA is an effective method for predicting circRNA-disease associations.
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Affiliation(s)
- Jing Yang
- School of Computer ScienceShaanxi Normal UniversityXi'anShaanxiChina
| | - Xiujuan Lei
- School of Computer ScienceShaanxi Normal UniversityXi'anShaanxiChina
| | - Fa Zhang
- School of Medical TechnologyBeijing Institute of TechnologyBeijingChina
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Jalali P, Samii A, Rezaee M, Shahmoradi A, Pashizeh F, Salehi Z. UBE2C: A pan-cancer diagnostic and prognostic biomarker revealed through bioinformatics analysis. Cancer Rep (Hoboken) 2024; 7:e2032. [PMID: 38577722 PMCID: PMC10995712 DOI: 10.1002/cnr2.2032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/03/2024] [Accepted: 02/22/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND The diverse and complex attributes of cancer have made it a daunting challenge to overcome globally and remains to endanger human life. Detection of critical cancer-related gene alterations in solid tumor samples better defines patient diagnosis and prognosis, and indicates what targeted therapies must be administered to improve cancer patients' outcome. MATERIALS AND METHODS To identify genes that have aberrant expression across different cancer types, differential expressed genes were detected within the TCGA datasets. Subsequently, the DEGs common to all pan cancers were determined. Furthermore, various methods were employed to gain genetic alterations, co-expression genes network and protein-protein interaction (PPI) network, pathway enrichment analysis of common genes. Finally, the gene regulatory network was constructed. RESULTS Intersectional analysis identified UBE2C as a common DEG between all 28 types of studied cancers. Upregulated UBE2C expression was significantly correlated with OS and DFS of 10 and 9 types of cancer patients. Also, UBE2C can be a diagnostic factor in CESC, CHOL, GBM, and UCS with AUC = 100% and diagnose 19 cancer types with AUC ≥90%. A ceRNA network constructed including UBE2C, 41 TFs, 10 shared miRNAs, and 21 circRNAs and 128 lncRNAs. CONCLUSION In summary, UBE2C can be a theranostic gene, which may serve as a reliable biomarker in diagnosing cancers, improving treatment responses and increasing the overall survival of cancer patients and can be a promising gene to be target by cancer drugs in the future.
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Affiliation(s)
- Pooya Jalali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Centre, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical SciencesTehranIran
| | - Amir Samii
- Department of Hematology and Blood TransfusionSchool of Allied Medical Sciences, Iran University of Medical SciencesTehranIran
| | - Malihe Rezaee
- Department of PharmacologySchool of Medicine, Shahid Beheshti University of Medical SciencesTehranIran
| | - Arvin Shahmoradi
- Department of Laboratory MedicineFaculty of Paramedical, Kurdistan University of Medical SciencesSanandajIran
| | - Fatemeh Pashizeh
- Department of Clinical ImmunologyShahid Sadoughi University of Medical SciencesYazdIran
| | - Zahra Salehi
- Hematology, Oncology and Stem Cell Transplantation Research Center, Tehran University of Medical SciencesTehranIran
- Research Institute for Oncology, Hematology and Cell Therapy, Tehran University of Medical SciencesTehranIran
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Gong B, Li M, Wang Z, Hao G, Sun L, Zhang J, Yuan L. Integrated analysis of circRNA- related ceRNA network targeting neuroinflammation in medial temporal lobe epilepsy. Brain Res Bull 2024; 209:110908. [PMID: 38402995 DOI: 10.1016/j.brainresbull.2024.110908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 02/04/2024] [Accepted: 02/21/2024] [Indexed: 02/27/2024]
Abstract
BACKGROUND medial temporal lobe epilepsy (mTLE) is among the most common types of temporal lobe epilepsy (TLE) ,it is generally resistant to drug treatment, which significantly impacts the quality of life and treatment. Research on novel therapeutic approaches for mTLE has become a current focus. Our study aims to construct and analyze a competing endogenous RNA (ceRNA) network that targets neuroinflammation using publicly available data, which may offer a novel therapeutic approach for mTLE. METHODS we utilized the R package to analyze GSE186334 downloaded from Gene Expression Omnibus database, subsequently constructing and identifying hub network within the ceRNA network using public databases. Lastly, we validated the expressions and interactions of some nodes within the hub ceRNA network in Sombati cell model. RESULTS our transcriptome analysis identified 649 differentially expressed (DE) mRNAs (273 up-regulated, 376 down-regulated) and 36 DE circRNAs (11 up-regulated, 25 down-regulated) among mTLE patients. A total of 23 candidate DE mRNAs associated with neuroinflammation were screened, and two ceRNA networks were constructed. A hub network was further screened which included 3 mRNAs, 22 miRNAs, and 11 circRNAs. Finally, we confirmed the hsa-miR-149-5p is crucial in the regulatory effect of hsa_circ_0005145 on IL - 1α in the hub network. CONCLUSIONS In summary, our study identified a hub ceRNA network and validated a potential circRNA-miRNA-mRNA axis targeting neuroinflammation. The results of our research may serve as a potential therapeutic target for mTLE.
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Affiliation(s)
- Bingzheng Gong
- The Second Affiliated Hospital of Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271000, China
| | - Mian Li
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250000, China
| | - Ziru Wang
- School of Clinical Medicine and Basic Medical Science, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250000, China
| | - Gulingyue Hao
- School of Clinical Medicine and Basic Medical Science, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250000, China
| | - Liang Sun
- College of Artificial Intelligence and Big Data for Medical Science, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250000, China.
| | - Jingjun Zhang
- School of Clinical Medicine and Basic Medical Science, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250000, China.
| | - Liangjie Yuan
- School of Clinical Medicine and Basic Medical Science, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250000, China.
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Wu M, Yuan H, Zou W, Xu S, Liu S, Gao Q, Guo Q, Han Y, An X. Circular RNAs: characteristics, functions, mechanisms, and potential applications in thyroid cancer. Clin Transl Oncol 2024; 26:808-824. [PMID: 37864677 DOI: 10.1007/s12094-023-03324-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 09/08/2023] [Indexed: 10/23/2023]
Abstract
Thyroid cancer (TC) is one of the most common endocrine malignancies, and its incidence has increased globally. Despite extensive research, the underlying molecular mechanisms of TC remain partially understood, warranting continued exploration of molecular markers for diagnostic and prognostic applications. Circular RNAs (circRNAs) have recently garnered significant attention owing to their distinct roles in cancers. This review article introduced the classification and biological functions of circRNAs and summarized their potential as diagnostic and prognostic markers in TC. Further, the interplay of circRNAs with PI3K/Akt/mTOR, Wnt/β-catenin, MAPK/ERK, Notch, JAK/STAT, and AMPK pathways is elaborated upon. The article culminates with an examination of circRNA's role in drug resistance of TC and highlights the challenges in circRNA research in TC.
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Affiliation(s)
- Mengmeng Wu
- Department of Thyroid Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China
| | - Haibin Yuan
- Department of Health Management, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China
| | - Weiwei Zou
- Department of Thyroid Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China
| | - Shujian Xu
- Department of Thyroid Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China
| | - Song Liu
- Department of Thyroid Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China
| | - Qiang Gao
- Department of Thyroid Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China
| | - Qingqun Guo
- Department of Thyroid Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China
| | - Yong Han
- Department of Thyroid Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China.
| | - Xingguo An
- Department of Thyroid Surgery, Binzhou Medical University Hospital, Binzhou, 256603, Shandong, People's Republic of China.
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Liu W, Li HM, Bai G. Construction of a novel mRNA-miRNA-lncRNA/circRNA triple subnetwork associated with immunity and aging in intervertebral disc degeneration. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2024:1-20. [PMID: 38555595 DOI: 10.1080/15257770.2024.2334353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 03/18/2024] [Indexed: 04/02/2024]
Abstract
OBJECTIVE Intervertebral disk degeneration (IVDD) is one of the most common causes of low back pain. However, in the etiology of IVDD, the specific method by which nucleus pulposus (NP) cell senescence and the immune response induce disease is uncertain. METHODS Gene Expression Omnibus database was used to find differentially expressed genes (DEGs), differentially expressed miRNAs (DE miRNAs), differentially expressed lncRNAs (DE lncRNAs), and differentially expressed circRNAs (DE circRNAs). Functional enrichment analysis was performed through Enrichr database. Potential regulatory miRNAs, lncRNAs and circRNAs of mRNAs were predicted by ENCORI and circBank, respectively. RESULTS We identified 198 upregulated and 131 downregulated genes, 39 upregulated and 22 downregulated miRNAs, 2152 upregulated and 564 downregulated lncRNAs, and 352 upregulated and 279 downregulated circRNAs as DEGs, DE miRNAs, DE lncRNAs, DE circRNAs, respectively. Functional enrichment analysis revealed that they were significantly enriched in Toll-like receptor signaling route and the NF-kappa B signaling pathway. An mRNA-miRNA-lncRNA/circRNA network linked to the pathogenesis of NP cells in IVDD was constructed based on node degree and differential expression level. Eight immune-related DEGs (6 upregulated and 2 downregulated genes) and five aging-related DEGs (3 upregulated and 2 downregulated genes) were identified in the critical network. CONCLUSION We established a novel immune-related and aging-related triple regulatory network of mRNA-miRNA-lncRNA/circRNA ceRNA, among which all RNAs may be utilized as the pathogenesis biomarker of NP cells in IVDD.
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Affiliation(s)
- Wei Liu
- Department of Orthopedics, the Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, Zhejiang, P R China
| | - Hui-Min Li
- Department of Orthopedics, the Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, Zhejiang, P R China
| | - Guangchao Bai
- Department of Orthopedics, the Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, Zhejiang, P R China
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DeSouza NR, Nielsen KJ, Jarboe T, Carnazza M, Quaranto D, Kopec K, Suriano R, Islam HK, Tiwari RK, Geliebter J. Dysregulated Expression Patterns of Circular RNAs in Cancer: Uncovering Molecular Mechanisms and Biomarker Potential. Biomolecules 2024; 14:384. [PMID: 38672402 PMCID: PMC11048371 DOI: 10.3390/biom14040384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 04/28/2024] Open
Abstract
Circular RNAs (circRNAs) are stable, enclosed, non-coding RNA molecules with dynamic regulatory propensity. Their biogenesis involves a back-splicing process, forming a highly stable and operational RNA molecule. Dysregulated circRNA expression can drive carcinogenic and tumorigenic transformation through the orchestration of epigenetic modifications via extensive RNA and protein-binding domains. These multi-ranged functional capabilities have unveiled extensive identification of previously unknown molecular and cellular patterns of cancer cells. Reliable circRNA expression patterns can aid in early disease detection and provide criteria for genome-specific personalized medicine. Studies described in this review have revealed the novelty of circRNAs and their biological ss as prognostic and diagnostic biomarkers.
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Affiliation(s)
- Nicole R. DeSouza
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (N.R.D.)
| | - Kate J. Nielsen
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (N.R.D.)
| | - Tara Jarboe
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (N.R.D.)
| | - Michelle Carnazza
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (N.R.D.)
| | - Danielle Quaranto
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (N.R.D.)
| | - Kaci Kopec
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (N.R.D.)
| | - Robert Suriano
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (N.R.D.)
- Division of Natural Sciences, University of Mount Saint Vincent, Bronx, NY 10471, USA
| | - Humayun K. Islam
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (N.R.D.)
| | - Raj K. Tiwari
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (N.R.D.)
- Department of Otolaryngology, New York Medical College, Valhalla, NY 10595, USA
| | - Jan Geliebter
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, NY 10595, USA; (N.R.D.)
- Department of Otolaryngology, New York Medical College, Valhalla, NY 10595, USA
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Liu D, Zhou X, He Y, Zhao J. The Roles of CircRNAs in Mitochondria. J Cancer 2024; 15:2759-2769. [PMID: 38577612 PMCID: PMC10988319 DOI: 10.7150/jca.92111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/02/2024] [Indexed: 04/06/2024] Open
Abstract
Mitochondria participate in varieties of cellular events. It is widely accepted that human mitochondrial genome encodes 13 proteins, 2 rRNAs, and 22 tRNAs. Gene variation derived from human nuclear genome cannot completely explain mitochondrial diseases. The advent of high-throughput sequencing coupled with novel bioinformatic analyses decode the complexity of mitochondria-derived transcripts. Recently, circular RNAs (circRNAs) from both human mitochondrial genome and nuclear genome have been found to be located at mitochondria. Studies about the roles and molecular mechanisms underlying trafficking of the nucleus encoded circRNAs to mitochondria and mitochondria encoded circRNAs to the nucleus or cytoplasm in mammals are only beginning to emerge. These circRNAs have been associated with a variety of diseases, especially cancers. Here, we discuss the emerging field of mitochondria-located circRNAs by reviewing their identification, expression patterns, regulatory roles, and functional mechanisms. Mitochondria-located circRNAs have regulatory roles in cellular physiology and pathology. We also highlight future perspectives and challenges in studying mitochondria-located circRNAs, as well as their potential biomedical applications.
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Affiliation(s)
- Donghong Liu
- Department of Special Medical Care, Third Affiliated Hospital of Naval Medical University, Shanghai, 200438, China
| | - Xinyu Zhou
- Department of Epidemiology, Naval Medical University, Shanghai, 200433, China
| | - Yida He
- Department of Epidemiology, Naval Medical University, Shanghai, 200433, China
| | - Jun Zhao
- Department of Special Medical Care, Third Affiliated Hospital of Naval Medical University, Shanghai, 200438, China
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Liu Q, Zhang Y, Han B, Wang M, Hu H, Ning J, Hu W, Chen M, Pang Y, Chen Y, Bao L, Niu Y, Zhang R. circRNAs deregulation in exosomes derived from BEAS-2B cells is associated with vascular stiffness induced by PM 2.5. J Environ Sci (China) 2024; 137:527-539. [PMID: 37980036 DOI: 10.1016/j.jes.2023.02.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 11/20/2023]
Abstract
As an environmental pollutant, ambient fine particulate matter (PM2.5) was linked to cardiovascular diseases. The molecular mechanisms underlying PM2.5-induced extrapulmonary disease has not been elucidated clearly. In this study the ambient PM2.5 exposure mice model we established was to explore adverse effects of vessel and potential mechanisms. Long-term PM2.5 exposure caused reduced lung function and vascular stiffness in mice. And chronic PM2.5 induced migration and epithelial-mesenchymal transition (EMT) phenotype in BEAS-2B cells. After PM2.5 treatment, the circRNAs and mRNAs levels of exosomes released by BEAS-2B cells were detected by competing endogenous RNA (ceRNA) array, which contained 1664 differentially expressed circRNAs (DE-circRNAs) and 308 differentially expressed mRNAs (DE-mRNAs). By bioinformatics analysis on host genes of DE-circRNAs, vascular diseases and some pathways related to vascular diseases including focal adhesion, tight junction and adherens junction were enriched. Then, ceRNA network was constructed, and DE-mRNAs in ceRNA network were conducted functional enrichment analysis by Ingenuity Pathway Analysis, which indicated that hsa_circ_0012627, hsa_circ_0053261 and hsa_circ_0052810 were related to vascular endothelial dysfunction. Furthermore, it was verified experimentally that ExoPM2.5 could induce endothelial dysfunction by increased endothelial permeability and decreased relaxation in vitro. In present study, we investigated in-depth knowledge into the molecule events related to PM2.5 toxicity and pathogenesis of vascular diseases.
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Affiliation(s)
- Qingping Liu
- Department of Toxicology, Hebei Medical University, Shijiazhuang 050017, China
| | - Yaling Zhang
- Department of Toxicology, Hebei Medical University, Shijiazhuang 050017, China
| | - Bin Han
- Department of Toxicology, Hebei Medical University, Shijiazhuang 050017, China; State Key Laboratory of Environment Health (Incubation), Key Laboratory of Environment and Health, Ministry of Education, Key Laboratory of Environment and Health (Wuhan), Ministry of Environmental Protection, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Mengruo Wang
- Department of Toxicology, Hebei Medical University, Shijiazhuang 050017, China
| | - Huaifang Hu
- Department of Toxicology, Hebei Medical University, Shijiazhuang 050017, China
| | - Jie Ning
- Department of Toxicology, Hebei Medical University, Shijiazhuang 050017, China
| | - Wentao Hu
- Department of Toxicology, Hebei Medical University, Shijiazhuang 050017, China
| | - Meiyu Chen
- Department of Toxicology, Hebei Medical University, Shijiazhuang 050017, China
| | - Yaxian Pang
- Department of Toxicology, Hebei Medical University, Shijiazhuang 050017, China
| | - Yuanyuan Chen
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention, Beijing 100021, China
| | - Lei Bao
- Occupational Health and Environmental Health, Hebei Medical University, Shijiazhuang 050017, China
| | - Yujie Niu
- Occupational Health and Environmental Health, Hebei Medical University, Shijiazhuang 050017, China; Hebei Key Laboratory of Environment and Human Health, Hebei Medical University, Shijiazhuang 050017, China
| | - Rong Zhang
- Department of Toxicology, Hebei Medical University, Shijiazhuang 050017, China; Hebei Key Laboratory of Environment and Human Health, Hebei Medical University, Shijiazhuang 050017, China.
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Petrova M, Margasyuk S, Vorobeva M, Skvortsov D, Dontsova O, Pervouchine DD. BRD2 and BRD3 genes independently evolved RNA structures to control unproductive splicing. NAR Genom Bioinform 2024; 6:lqad113. [PMID: 38226395 PMCID: PMC10789245 DOI: 10.1093/nargab/lqad113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 12/13/2023] [Accepted: 12/28/2023] [Indexed: 01/17/2024] Open
Abstract
The mammalian BRD2 and BRD3 genes encode structurally related proteins from the bromodomain and extraterminal domain protein family. The expression of BRD2 is regulated by unproductive splicing upon inclusion of exon 3b, which is located in the region encoding a bromodomain. Bioinformatic analysis indicated that BRD2 exon 3b inclusion is controlled by a pair of conserved complementary regions (PCCR) located in the flanking introns. Furthermore, we identified a highly conserved element encoding a cryptic poison exon 5b and a previously unknown PCCR in the intron between exons 5 and 6 of BRD3, however, outside of the homologous bromodomain. Minigene mutagenesis and blockage of RNA structure by antisense oligonucleotides demonstrated that RNA structure controls the rate of inclusion of poison exons. The patterns of BRD2 and BRD3 expression and splicing show downregulation upon inclusion of poison exons, which become skipped in response to transcription elongation slowdown, further confirming a role of PCCRs in unproductive splicing regulation. We conclude that BRD2 and BRD3 independently acquired poison exons and RNA structures to dynamically control unproductive splicing. This study describes a convergent evolution of regulatory unproductive splicing mechanisms in these genes, providing implications for selective modulation of their expression in therapeutic applications.
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Affiliation(s)
- Marina Petrova
- Skolkovo Institute of Science and Technology, Bolshoy Bulvar, 30, str. 1, Moscow 121205, Russia
| | - Sergey Margasyuk
- Skolkovo Institute of Science and Technology, Bolshoy Bulvar, 30, str. 1, Moscow 121205, Russia
| | - Margarita Vorobeva
- Faculty of Chemistry, Moscow State University, GSP-1, 1-3 Leninskiye Gory, Moscow 119991, Russia
| | - Dmitry Skvortsov
- Skolkovo Institute of Science and Technology, Bolshoy Bulvar, 30, str. 1, Moscow 121205, Russia
- Faculty of Chemistry, Moscow State University, GSP-1, 1-3 Leninskiye Gory, Moscow 119991, Russia
| | - Olga A Dontsova
- Skolkovo Institute of Science and Technology, Bolshoy Bulvar, 30, str. 1, Moscow 121205, Russia
- Faculty of Chemistry, Moscow State University, GSP-1, 1-3 Leninskiye Gory, Moscow 119991, Russia
| | - Dmitri D Pervouchine
- Skolkovo Institute of Science and Technology, Bolshoy Bulvar, 30, str. 1, Moscow 121205, Russia
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Li Y, Wang B, Sun W, Kong C, Ding J, Hu F, Li J, Chen X, Lu S. Construction of circ_0071922-miR-15a-5p-mRNA network in intervertebral disc degeneration by RNA-sequencing. JOR Spine 2024; 7:e1275. [PMID: 38222808 PMCID: PMC10782064 DOI: 10.1002/jsp2.1275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/25/2023] [Accepted: 07/19/2023] [Indexed: 01/16/2024] Open
Abstract
Background Low back pain (LBP) is the main factor of global disease burden. Intervertebral disc degeneration (IVDD) has long been known as the leading reason of LBP. Increasing studies have verified that circular RNAs (circRNAs)-microRNAs (miRNAs)-mRNAs network is widely involved in the pathological processes of IVDD. However, no study was made to demonstrate the circRNAs-mediated ferroptosis, oxidative stress, extracellular matrix metabolism, and immune response in IVDD. Methods We collected 3 normal and 3 degenerative nucleus pulposus tissues to conduct RNA-sequencing to identify the key circRNAs and miRNAs in IVDD. Bioinformatics analysis was then conducted to construct circRNAs-miRNAs-mRNAs interaction network associated with ferroptosis, oxidative stress, extracellular matrix metabolism, and immune response. We also performed animal experiments to validate the therapeutic effects of key circRNAs in IVDD. Results We found that circ_0015435 was most obviously upregulated and circ_0071922 was most obviously downregulated in IVDD using RNA-sequencing. Then we observed that hsa-miR-15a-5p was the key downstream of circ_0071922, and hsa-miR-15a-5p was the top upregulated miRNA in IVDD. Bioinformatics analysis was conducted to predict that 56 immunity-related genes, 29 ferroptosis-related genes, 23 oxidative stress-related genes and 8 ECM-related genes are the targets mRNAs of hsa-miR-15a-5p. Then we constructed a ceRNA network encompassing 24 circRNAs, 6 miRNAs, and 101 mRNAs. Additionally, we demonstrated that overexpression of circ_0071922 can alleviate IVDD progression in a rat model. Conclusions The findings of this study suggested that circ_0071922-miR-15a-5p-mRNA signaling network might affect IVDD by modulating the nucleus pulposus cells ferroptosis, oxidative stress, ECM metabolism, and immune response, which is an effective therapeutic targets of IVDD.
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Affiliation(s)
- Yongjin Li
- Department of OrthopedicsXuanwu Hospital, Capital Medical UniversityBeijingChina
- National Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Baobao Wang
- Department of OrthopedicsXuanwu Hospital, Capital Medical UniversityBeijingChina
- National Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Wenzhi Sun
- Department of OrthopedicsXuanwu Hospital, Capital Medical UniversityBeijingChina
- National Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Chao Kong
- Department of OrthopedicsXuanwu Hospital, Capital Medical UniversityBeijingChina
- National Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Junzhe Ding
- Department of OrthopedicsXuanwu Hospital, Capital Medical UniversityBeijingChina
- National Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Feng Hu
- Spine Center, Department of Orthopaedics, The First Affiliated Hospital of USTC, Division of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhuiChina
| | - Jianhua Li
- Department of OrthopedicsTianjin Haihe HospitalTianjinChina
| | - Xiaolong Chen
- Department of OrthopedicsXuanwu Hospital, Capital Medical UniversityBeijingChina
- National Clinical Research Center for Geriatric DiseasesBeijingChina
| | - Shibao Lu
- Department of OrthopedicsXuanwu Hospital, Capital Medical UniversityBeijingChina
- National Clinical Research Center for Geriatric DiseasesBeijingChina
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Liu J, Li J, Jin F, Li Q, Zhao G, Wu L, Li X, Xia J, Cheng N. dbCRAF: a curated knowledgebase for regulation of radiation response in human cancer. NAR Cancer 2024; 6:zcae008. [PMID: 38406264 PMCID: PMC10894039 DOI: 10.1093/narcan/zcae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/10/2023] [Accepted: 02/15/2024] [Indexed: 02/27/2024] Open
Abstract
Radiation therapy (RT) is one of the primary treatment modalities of cancer, with 40-60% of cancer patients benefiting from RT during their treatment course. The intrinsic radiosensitivity or acquired radioresistance of tumor cells would affect the response to RT and clinical outcomes in patients. Thus, mining the regulatory mechanisms in tumor radiosensitivity or radioresistance that have been verified by biological experiments and computational analysis methods will enhance the overall understanding of RT. Here, we describe a comprehensive database dbCRAF (http://dbCRAF.xialab.info/) to document and annotate the factors (1,677 genes, 49 proteins and 612 radiosensitizers) linked with radiation response, including radiosensitivity, radioresistance in cancer cells and prognosis in cancer patients receiving RT. On the one hand, dbCRAF enables researchers to directly access knowledge for regulation of radiation response in human cancer buried in the vast literature. On the other hand, dbCRAF provides four flexible modules to analyze and visualize the functional relationship between these factors and clinical outcome, KEGG pathway and target genes. In conclusion, dbCRAF serves as a valuable resource for elucidating the regulatory mechanisms of radiation response in human cancers as well as for the improvement of RT options.
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Affiliation(s)
- Jie Liu
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Jing Li
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Fangfang Jin
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Qian Li
- School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Guoping Zhao
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Lijun Wu
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Xiaoyan Li
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Junfeng Xia
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China
| | - Na Cheng
- School of Biomedical Engineering, Anhui Medical University, Hefei, Anhui 230032, China
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Meng X, Li W, Yu T, Lu F, Wang C, Yuan H, Yang W, Dong W, Xiao W, Zhang X. Hsa_circ_0086414/transducer of ERBB2 (TOB2) axis-driven lipid elimination and tumor suppression in clear cell renal cell cancer via perilipin 3. Int J Biol Macromol 2024; 261:129636. [PMID: 38272402 DOI: 10.1016/j.ijbiomac.2024.129636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 12/15/2023] [Accepted: 12/23/2023] [Indexed: 01/27/2024]
Abstract
BACKGROUND Renal cell cancer (RCC) is characterized by abnormal lipid accumulation. However, the specific mechanism by which such lipid deposition is eliminated remains unclear. Circular RNAs (circRNAs) widely regulate various biological processes, but the effect of circRNAs on lipid metabolism in cancers, especially clear cell renal cell carcinoma (ccRCC), remains poorly understood. METHODS The downregulated circRNA, hsa_circ_0086414, was identified from high-throughput RNA-sequencing data of human ccRCC and pair-matched normal tissues. The target relationship between circRNA_0086414 and miR-661, and the transducer of ERBB2 (TOB2) was predicted using publicly available software programs and verified by luciferase reporter assays. The clinical prognostic value of TOB2 was evaluated by bioinformatic analysis. The expression levels of circRNA_0086414, miR-661, TOB2, and perilipin 3 (PLIN3) were measured by quantitative reverse-transcription polymerase chain reaction or western blot analysis. Cell Counting Kit-8, transwell assays, and xenograft models were employed to assess the biological behaviors of the hsa_circ_0086414/TOB2 axis. Oil Red staining and triglyceride assay was conducted to assess lipid deposition. RESULTS Herein, we identified a downregulated circRNA, hsa_circ_0086414. Functionally, the restored hsa_circ_0086414 inhibited ccRCC proliferation, metastasis, and lipid accumulation in vitro and in vivo. Furthermore, the downregulated TOB2 predicted adverse prognosis and promoted cancer progression and lipid deposition in ccRCC. Mechanically, the binding of hsa_circ_0086414 to miR-661, as a miRNA sponge, upregulates the expression of TOB2, wielding an anti-oncogene effect. Importantly, the restored hsa_circ_0086414/TOB2 axis significantly contributed to the elimination of lipid deposition by inhibiting the lipid metabolism regulator PLIN3 in ccRCC cells. CONCLUSIONS Our data highlight the importance of the hsa_circ_0086414/TOB2/PLIN3 axis as a tumor suppressor and lipid eliminator in ccRCC. The positive modulation of the hsa_circ_0086414/TOB2 axis might lead to the development of novel treatment strategies for ccRCC.
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Affiliation(s)
- Xiangui Meng
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen 518000, China; Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Weiquan Li
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen 518000, China; Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Tiexi Yu
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen 518000, China; Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Feiyi Lu
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen 518000, China; Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Cheng Wang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen 518000, China; Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Hongwei Yuan
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen 518000, China; Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Wei Yang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen 518000, China; Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Wei Dong
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen 518000, China; Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| | - Wen Xiao
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen 518000, China; Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
| | - Xiaoping Zhang
- Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen 518000, China; Institute of Urology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China.
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46
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He A, Liao F, Lin X. Circ_0007351 Exerts an Oncogenic Role In Colorectal Cancer Depending on the Modulation of the miR-5195-3p/GPRC5A Cascade. Mol Biotechnol 2024:10.1007/s12033-024-01071-3. [PMID: 38386274 DOI: 10.1007/s12033-024-01071-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/08/2024] [Indexed: 02/23/2024]
Abstract
Circular RNAs (circRNAs) exert critical functions in colorectal cancer development. In this work, we wanted to elucidate the functional role and regulatory mechanism of circ_0007351 in colorectal cancer. For quantification of circ_0007351, microRNA (miR)-5195-3p and G Protein-coupled receptor class C group 5 member A (GPRC5A), a qRT-PCR, immunoblotting or immunohistochemistry assay was performed. Effects of circ_0007351/miR-5195-3p/GPRC5A cascade were evaluated by determining cell viability, proliferation, colony formation, motility, and invasion. Relationships among variables were assessed by dual-luciferase reporter assay. Animal studies were performed to evaluate circ_0007351's function in the growth of xenograft tumors. Circ_0007351 was markedly up-regulated in colorectal cancer tissues and cells. Down-regulation of circ_0007351 hindered cell growth, migration and invasiveness. Also, circ_0007351 depletion exerted a suppressive function in colorectal cell xenograft growth in vivo. Mechanistically, circ_0007351 sponged miR-5195-3p to sequester miR-5195-3p. Reduction of available miR-5195-3p neutralized the effects of circ_0007351 down-regulation on cell phenotypes. MiR-5195-3p directly targeted and inhibited GPRC5A. Circ_0007351 regulated GPRC5A expression by sponging miR-5195-3p. Moreover, the effects of circ_0007351 down-regulation on cell functional phenotypes were due to in part the reduction of GPRC5A expression. Our findings show that circ_0007351 down-regulation impedes proliferation, motility, and invasiveness in colorectal cancer cells at least in part via the regulation of the miR-5195-3p/GPRC5A cascade, highlighting that circ_0007351 inhibition may have a potential therapeutic value for colorectal cancer.
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Affiliation(s)
- Aijun He
- Oncology Department, People's Hospital of Shenzhen Baoan District, NO. 118, Longjing Road, Baoan District, Shenzhen, 518100, China
| | - Fangxin Liao
- Oncology Department, People's Hospital of Shenzhen Nanshan, Shenzhen, 518100, China
| | - Xiaohui Lin
- Oncology Department, People's Hospital of Shenzhen Baoan District, NO. 118, Longjing Road, Baoan District, Shenzhen, 518100, China.
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Barbosa DF, Oliveira LS, Nachtigall PG, Valentini Junior R, de Souza N, Paschoal AR, Kashiwabara AY. cirCodAn: A GHMM-based tool for accurate prediction of coding regions in circRNA. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 139:289-334. [PMID: 38448139 DOI: 10.1016/bs.apcsb.2023.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Studies focusing on characterizing circRNAs with the potential to translate into peptides are quickly advancing. It is helping to elucidate the roles played by circRNAs in several biological processes, especially in the emergence and development of diseases. While various tools are accessible for predicting coding regions within linear sequences, none have demonstrated accurate open reading frame detection in circular sequences, such as circRNAs. Here, we present cirCodAn, a novel tool designed to predict coding regions in circRNAs. We evaluated the performance of cirCodAn using datasets of circRNAs with strong translation evidence and showed that cirCodAn outperformed the other tools available to perform a similar task. Our findings demonstrate the applicability of cirCodAn to identify coding regions in circRNAs, which reveals the potential of use of cirCodAn in future research focusing on elucidating the biological roles of circRNAs and their encoded proteins. cirCodAn is freely available at https://github.com/denilsonfbar/cirCodAn.
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Affiliation(s)
- Denilson Fagundes Barbosa
- Programa de Pós-Graduação Associado em Bioinformática (UFPR/UTFPR), Departamento Acadêmico de Computação (DACOM), Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Paraná, Brazil; Instituto Federal de Educação, Ciência e Tecnologia de Santa Catarina (IFSC), Canoinhas, Santa Catarina, Brazil
| | - Liliane Santana Oliveira
- Programa de Pós-Graduação Associado em Bioinformática (UFPR/UTFPR), Departamento Acadêmico de Computação (DACOM), Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Paraná, Brazil
| | - Pedro Gabriel Nachtigall
- Laboratório de Toxinologia Aplicada, CeTICS, Instituto Butantan, São Paulo, SP, Brazil; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Rodolpho Valentini Junior
- Programa de Pós-Graduação Associado em Bioinformática (UFPR/UTFPR), Departamento Acadêmico de Computação (DACOM), Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Paraná, Brazil
| | - Nayane de Souza
- Programa de Pós-Graduação Associado em Bioinformática (UFPR/UTFPR), Departamento Acadêmico de Computação (DACOM), Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Paraná, Brazil
| | - Alexandre Rossi Paschoal
- Programa de Pós-Graduação Associado em Bioinformática (UFPR/UTFPR), Departamento Acadêmico de Computação (DACOM), Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Paraná, Brazil
| | - André Yoshiaki Kashiwabara
- Programa de Pós-Graduação Associado em Bioinformática (UFPR/UTFPR), Departamento Acadêmico de Computação (DACOM), Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Paraná, Brazil.
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48
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Li F, Du WW, Li X, Xu J, Wu N, Awan FM, Yang Y, Alashti FA, Wang S, Yang BB. A Novel Circular RNA circITGa9 Predominantly Generated in Human Heart Disease Induces Cardiac Remodeling and Fibrosis. RESEARCH (WASHINGTON, D.C.) 2024; 7:0303. [PMID: 38323094 PMCID: PMC10845611 DOI: 10.34133/research.0303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/27/2023] [Indexed: 02/08/2024]
Abstract
Recent studies have highlighted the pivotal roles of circular RNAs (circRNAs) in cardiovascular diseases. Through high-throughput circRNA sequencing of both normal myocardial tissues and hypertrophic patients, we unveiled 32,034 previously undiscovered circRNAs with distinct cardiac expression patterns. Notably, circITGa9, a circRNA derived from integrin-α9, exhibited substantial up-regulation in cardiac hypertrophy patients. This elevation was validated across extensive sample pools from cardiac patients and donors. In vivo experiments revealed heightened cardiac fibrosis in mice subjected to transverse aortic constriction (TAC) after circITGa9 injection. We identified circITGa9 binding proteins through circRNA precipitation followed by liquid chromatography tandem-mass spectrometry. Furthermore, circRNA pull-down/precipitation assays demonstrated that increased circITGa9 expression facilitated binding with tropomyosin 3 (TPM3). Specific binding sites between circITGa9 and TPM3 were identified through computational algorithms and further validated by site-directed mutagenesis. We further showed that circITGa9 induced actin polymerization, characteristic of tissue fibrosis. Finally, we developed approaches that improved cardiac function and decreased fibrosis by delivering small interfering RNA targeting circITGa9 or blocking oligo inhibiting the interaction of circITGa9 and TPM3 into TAC mice, which is amenable for further preclinical and translational development. We conclude that elevated circITGa9 levels drive cardiac remodeling and fibrosis. By pinpointing circITGa9 as a therapeutic target, we open doors to innovative interventions for mitigating cardiac remodeling and fibrosis.
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Affiliation(s)
- Feiya Li
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology,
University of Toronto, Toronto, ON, Canada
| | - William W. Du
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology,
University of Toronto, Toronto, ON, Canada
| | - Xiangmin Li
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology,
University of Toronto, Toronto, ON, Canada
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Safety and Health, National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Institute of Microbiology,
Guangdong Academy of Sciences, Guangzhou 510070, China
| | - Jindong Xu
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology,
University of Toronto, Toronto, ON, Canada
- Department of Anesthesiology, Guangdong Cardiovascular Institute,
Guangdong Provincial People’s Hospital & Guangdong Academy of Medical Sciences, Guangzhou, Guangdong Province, China
| | - Nan Wu
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology,
University of Toronto, Toronto, ON, Canada
| | - Faryal Mehwish Awan
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology,
University of Toronto, Toronto, ON, Canada
- Department of Medical Lab Technology,
The University of Haripur, Haripur, Pakistan
| | - Yang Yang
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology,
University of Toronto, Toronto, ON, Canada
| | - Fariborz Asghari Alashti
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology,
University of Toronto, Toronto, ON, Canada
| | - Sheng Wang
- Department of Anesthesiology, Beijing Anzhen Hospital,
Capital Medical University, Beijing, China
| | - Burton B. Yang
- Sunnybrook Research Institute and Department of Laboratory Medicine and Pathobiology,
University of Toronto, Toronto, ON, Canada
- Institute of Medical Sciences,
University of Toronto, Toronto, ON, Canada
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49
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Wang Z, She D, Liu L, Hua X, Zhu H, Yu L, Wang H, Zhu Y, Fan G, Wang Y, Xu M, Zhou G. Circular RNA CircSATB2 facilitates osteosarcoma progression through regulating the miR-661/FUS-mediated mRNA of ZNFX1. Cell Signal 2024; 114:110977. [PMID: 37984605 DOI: 10.1016/j.cellsig.2023.110977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/03/2023] [Accepted: 11/13/2023] [Indexed: 11/22/2023]
Abstract
Circular RNAs (circRNAs) are a class of non-coding RNAs which take part in the regulation of the initiation and development of different types of cancer. Numerous studies have demonstrated that circRNAs are involved in the progression of osteosarcoma (OS) as well. Thus, we put our emphasis on the exploration of crucial circRNAs in the process of OS initiation and progression. Using RNA sequencing, we found that circSATB2 was highly expressed in OS tissues compared with adjacent normal tissues. Then, we confirmed the high expression of circSATB2 in OS cell lines and OS tissues and its high expression was related to poor prognosis of OS patients. Functional experiments exhibited that circSATB2 promoted OS proliferation and migration in vitro, primary OS model and OS lung metastasis model showed that circSATB2 aggravated OS progression in vivo. Mechanistically, circSATB2 was found to promote OS progression through sponging miR-661 and FUS regulating the mRNA of ZNFX1. Therefore, circSATB2 could act as a prognostic marker and a therapeutic target for osteosarcoma in the future.
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Affiliation(s)
- Zhen Wang
- Department of Orthopaedics, Jinling Hospital, Nanjing University, Nanjing, China; Department of Orthopaedics, Jinling Hospital, Nanjing Medical University, Nanjing, China; Department of Orthopaedics, The General Hospital of Chinese People's Liberation Army, Beijing, China
| | - Diankun She
- Department of Orthopaedics, Jinling Hospital, Nanjing Medical University, Nanjing, China
| | - Lei Liu
- Department of Orthopedics,The Affiliated Yixing Hospital of Jiangsu University, Yixing, Jiangsu, China
| | - Xianming Hua
- Department of Orthopaedics, Jinling Hospital, Nanjing University, Nanjing, China
| | - Hao Zhu
- Department of Orthopaedics, Jinling Hospital, Nanjing University, Nanjing, China
| | - Lingfeng Yu
- Department of Orthopaedics, Jinling Hospital, Nanjing University, Nanjing, China
| | - Han Wang
- Department of Pharmacy, Jinling Hospital, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yan Zhu
- Department of Orthopaedics, Jinling Hospital, Nanjing Medical University, Nanjing, China
| | - Gentao Fan
- Department of Orthopaedics, Jinling Hospital, Nanjing Medical University, Nanjing, China
| | - Yicun Wang
- Department of Orthopaedics, Jinling Hospital, Nanjing University, Nanjing, China
| | - Meng Xu
- Department of Orthopaedics, The General Hospital of Chinese People's Liberation Army, Beijing, China.
| | - Guangxin Zhou
- Department of Orthopaedics, Jinling Hospital, Nanjing University, Nanjing, China; Department of Orthopaedics, Jinling Hospital, Nanjing Medical University, Nanjing, China.
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50
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Xie Q, Ma Y, Ren Z, Gu T, Jiang Z. Circular RNA: A new expectation for cardiovascular diseases. J Cell Biochem 2024; 125:e30512. [PMID: 38098251 DOI: 10.1002/jcb.30512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/14/2023] [Accepted: 11/30/2023] [Indexed: 01/30/2024]
Abstract
Circular RNA (circRNA) is a class of RNA with the 5' and 3' ends connected covalently to form a closed loop structure and characterized by high stability, conserved sequences and tissue specificity, which is caused by special reverse splicing methods. Currently, it has become a hot spot for research. With the discovery of its powerful regulatory functions and roles, the molecular mechanisms and future value of circRNA in participating in and regulating biological and pathological processes are becoming increasingly apparent. Among them is the increasing prevalence of cardiovascular diseases (CVDs). Many studies have elucidated that circRNA plays a crucial role in the development and progression of CVDs. Therefore, circRNA shows its advantages and brilliant expectations in the field of CVDs. In this review, we describe the biogenesis, bioinformatics detection and function of circRNA and discuss the role of circRNA and its effects on CVDs, including atherosclerosis, myocardial infarction, cardiac hypertrophy and heart failure, myocardial fibrosis, cardiac senescence, pulmonary hypertension, and diabetic cardiomyopathy by different mechanisms. That shows circRNA advantages and brilliant expectations in the field of CVDs.
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Affiliation(s)
- Qiao Xie
- Institute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Yun Ma
- Institute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, Hunan, China
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Zhong Ren
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Tianhe Gu
- Institute of Biochemistry and Molecular Biology, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Zhisheng Jiang
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, Hunan International Scientific and Technological Cooperation Base of Arteriosclerotic Disease, Hengyang Medical School, University of South China, Hengyang, Hunan, China
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